701
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Yu H, Bai L, Tang G, Wang X, Huang M, Cao G, Wang J, Luo Y. Novel Assay for Quantitative Analysis of DNA Methylation at Single-Base Resolution. Clin Chem 2019; 65:664-673. [PMID: 30737203 DOI: 10.1373/clinchem.2018.298570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/22/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND The DNA methylation profile provides valuable biological information with potential clinical utility. Several methods, such as quantitative methylation-specific PCR (qMSP), have been developed to examine methylation of specific CpG sites. Existing qMSP-based techniques fail to examine the genomic methylation at a single-base resolution, particularly for loci in gene bodies or extensive CpG open seas lacking flanking CpGs. Therefore, we established a novel assay for quantitative analysis of single-base methylation. METHODS To achieve a robust single-base specificity, we developed a PCR-based method using paired probes following bisulfite treatment. The 6-carboxyfluorescein- and 2'-chloro-7'phenyl-1,4-dichloro-6-carboxy-fluorescein-labeled probes conjugated with minor groove binder were designed to specifically bind to the methylated and unmethylated allele of targeted single CpGs at their 3' half regions, respectively. The methylation percentage was calculated by values of methylation / (methylation + unmethylation). RESULTS In the detection of single CpGs within promoters or bodies of 4 human genes, the quantitative analysis of the single-base methylation assay showed a detection capability in the 1 to 1:10000 dilution experiments with linearity over 4 orders of magnitude (R 2 = 0.989-0.994; all P < 0.001). In a cohort of 10 colorectal cancer samples, the assay showed a comparable detection performance with bisulfite pyrosequencing (R 2 = 0.875-0.990; all P < 0.001), which was better than conventional qMSP methods normalized by input control reaction (R 2 = 0.841 vs 0.769; P = 0.002 vs 0.009). CONCLUSIONS This assay is highly specific and sensitive for determining single-base methylation and, thus, is potentially useful for methylation-based panels in diagnostic and prognostic applications.
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Affiliation(s)
- Huichuan Yu
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Liangliang Bai
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Guannan Tang
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaolin Wang
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Meijin Huang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Guangwen Cao
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Jianping Wang
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yanxin Luo
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; .,Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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702
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Exploring the effect of antenatal depression treatment on children's epigenetic profiles: findings from a pilot randomized controlled trial. Clin Epigenetics 2019; 11:18. [PMID: 30717815 PMCID: PMC6360775 DOI: 10.1186/s13148-019-0616-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 01/14/2019] [Indexed: 11/10/2022] Open
Abstract
Background Children prenatally exposed to maternal depression more often show behavioral and emotional problems compared to unexposed children, possibly through epigenetic alterations. Current evidence is largely based on animal and observational human studies. Therefore, evidence from experimental human studies is needed. In this follow-up of a small randomized controlled trial (RCT), DNA-methylation was compared between children of women who had received cognitive behavioral therapy (CBT) for antenatal depression and children of women who had received treatment as usual (TAU). Originally, 54 women were allocated to CBT or TAU. A beneficial treatment effect was found on women’s mood symptoms. Findings We describe DNA methylation findings in buccal swab DNA of the 3–7-year-old children (CBT(N) = 12, TAU(N) = 11), at a genome-wide level at 770,668 CpG sites and at 729 CpG sites spanning 16 a priori selected candidate genes, including the glucocorticoid receptor (NR3C1). We additionally explored associations with women’s baseline depression and anxiety symptoms and offspring DNA methylation, regardless of treatment. Children from the CBT group had overall lower DNA methylation compared to children from the TAU group (mean ∆β = − 0.028, 95% CI − 0.035 to − 0.022). Although 68% of the promoter-associated NR3C1 probes were less methylated in the CBT group, with cg26464411 as top most differentially methylated CpG site (p = 0.038), mean DNA methylation of all NR3C1 promoter-associated probes did not differ significantly between the CBT and TAU groups (mean ∆β = 0.002, 95%CI − 0.010 to 0.011). None of the effects survived correction for multiple testing. There were no differences in mean DNA methylation between the children born to women with more severe depression or anxiety compared to children born to women with mild symptoms of depression or anxiety at baseline (mean ∆β (depression) = 0.0008, 95% CI − 0.007 to 0.008; mean ∆β (anxiety) = 0.0002, 95% CI − 0.004 to 0.005). Conclusion We found preliminary evidence of a possible effect of CBT during pregnancy on widespread methylation in children’s genomes and a trend toward lower methylation of a CpG site previously shown by others to be linked to depression and child maltreatment. However, none of the effects survived correction for multiple testing and larger studies are warranted. Trial registration Trial registration of the original RCT: ACTRN12607000397415. Registered on 2 August 2007.
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703
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Bardi N, Carbone F, Montecucco F. New insights into the role of DNA methylation in cardiovascular disease. Eur J Clin Invest 2019; 49:e13051. [PMID: 30456808 DOI: 10.1111/eci.13051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/14/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Nicholas Bardi
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Federico Carbone
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Fabrizio Montecucco
- First Clinic of Internal Medicine, Department of Internal Medicine and Centre of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, Italy.,IRCCS Ospedale Policlinico San Martino Genoa-Italian Cardiovascular Network, Genoa, Italy
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704
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Du Q, Bert SA, Armstrong NJ, Caldon CE, Song JZ, Nair SS, Gould CM, Luu PL, Peters T, Khoury A, Qu W, Zotenko E, Stirzaker C, Clark SJ. Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer. Nat Commun 2019; 10:416. [PMID: 30679435 PMCID: PMC6345877 DOI: 10.1038/s41467-019-08302-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 12/27/2018] [Indexed: 11/08/2022] Open
Abstract
DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and integrated epigenome analyses and demonstrate that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing. A subset of altered replication timing domains are conserved across cancers from different tissue origins. Notably, late-replicating regions in cancer cells display a loss of DNA methylation, and a switch in heterochromatin features from H3K9me3-marked constitutive to H3K27me3-marked facultative heterochromatin. Finally, analysis of 214 prostate and 35 breast cancer genomes reveal that late-replicating regions are prone to cis and early-replication to trans chromosomal rearrangements. Together, our data suggests that the nature of chromosomal rearrangement in cancer is related to the spatial and temporal positioning and altered epigenetic states of early-replicating compared to late-replicating loci.
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Affiliation(s)
- Qian Du
- Epigenetics Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, 2010, NSW, Australia
| | - Saul A Bert
- Epigenetics Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Nicola J Armstrong
- Mathematics and Statistics, School of Engineering and Information Technology, Murdoch University, Perth, 6150, WA, Australia
| | - C Elizabeth Caldon
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, 2010, NSW, Australia
- Replication and Genome Stability, Cancer Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Jenny Z Song
- Epigenetics Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Shalima S Nair
- Epigenetics Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Cathryn M Gould
- Epigenetics Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Phuc-Loi Luu
- Epigenetics Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Timothy Peters
- Epigenetics Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Amanda Khoury
- Epigenetics Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, 2010, NSW, Australia
| | - Wenjia Qu
- Epigenetics Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Elena Zotenko
- Epigenetics Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Clare Stirzaker
- Epigenetics Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, 2010, NSW, Australia
| | - Susan J Clark
- Epigenetics Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, 2010, NSW, Australia.
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705
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Curtis SW, Cobb DO, Kilaru V, Terrell ML, Kennedy EM, Marder ME, Barr DB, Marsit CJ, Marcus M, Conneely KN, Smith AK. Exposure to polybrominated biphenyl (PBB) associates with genome-wide DNA methylation differences in peripheral blood. Epigenetics 2019; 14:52-66. [PMID: 30676242 DOI: 10.1080/15592294.2019.1565590] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In 1973, Michigan residents were exposed to polybrominated biphenyl (PBB) when it was accidentally added to farm animal feed. Highly exposed individuals and their children have experienced endocrine-related health problems, though the underlying mechanism behind these remains unknown. We investigated whether PBB exposure is associated with variation in DNA methylation in peripheral blood samples from 658 participants of the Michigan PBB registry using the MethylationEPIC BeadChip, as well as investigated what the potential function of the affected regions are and whether these epigenetic marks are known to associate with endocrine system pathways. After multiple test correction (FDR <0.05), 1890 CpG sites associated with total PBB levels. These CpGs were not enriched in any particular biological pathway, but were enriched in enhancer and insulator regions, and depleted in regions near the transcription start site or in CpG islands (p < 0.05). They were also more likely to be in ARNT and ESR2 transcription factor binding sites (p = 3.27e-23 and p = 1.62e-6, respectively), and there was significant overlap between CpGs associated with PBB and CpGs associated with estrogen (p < 2.2e-16). PBB-associated CpGs were also enriched for CpGs known to be associated with gene expression in blood (eQTMs) (p < 0.05). These eQTMs were enriched for pathways related to immune function and endocrine-related autoimmune disease (FDR <0.05). These results indicate that exposure to PBB is associated with differences in epigenetic marks that suggest that it is acting similarly to estrogen and is associated with dysregulated immune system pathways.
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Affiliation(s)
- Sarah W Curtis
- a Genetics and Molecular Biology Program, Laney Graduate SchoolLaney Graduate School , Emory University School of Medicine , Atlanta , GA , USA
| | - Dawayland O Cobb
- b Department of Gynecology and Obstetrics , Emory University School of Medicine , Atlanta , GA , USA
| | - Varun Kilaru
- b Department of Gynecology and Obstetrics , Emory University School of Medicine , Atlanta , GA , USA
| | - Metrecia L Terrell
- c Department of Epidemiology , Emory University Rollins School of Public Health , Atlanta , GA , USA
| | - Elizabeth M Kennedy
- d Department of Environmental Health , Emory University Rollins School of Public Health , Atlanta , GA , USA
| | - M Elizabeth Marder
- d Department of Environmental Health , Emory University Rollins School of Public Health , Atlanta , GA , USA
| | - Dana Boyd Barr
- d Department of Environmental Health , Emory University Rollins School of Public Health , Atlanta , GA , USA
| | - Carmen J Marsit
- d Department of Environmental Health , Emory University Rollins School of Public Health , Atlanta , GA , USA
| | - Michele Marcus
- e Departments of Epidemiology, Environmental Health , Emory University Rollins School of Public Health , Atlanta , GA , USA.,f Department of Pediatrics , Emory University School of Medicine , Atlanta , GA , USA
| | - Karen N Conneely
- g Department of Human Genetics , Emory University School of Medicine , Atlanta , GA , USA
| | - Alicia K Smith
- a Genetics and Molecular Biology Program, Laney Graduate SchoolLaney Graduate School , Emory University School of Medicine , Atlanta , GA , USA.,b Department of Gynecology and Obstetrics , Emory University School of Medicine , Atlanta , GA , USA.,h Department of Psychiatry and Behavioral Science , Emory University School of Medicine , Atlanta , GA , USA
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706
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Hegi ME, Kleihues P, Wen PY, Suvà ML. Toward methylation-based classification of central nervous system tumors. Neuro Oncol 2019; 20:579-581. [PMID: 29584921 DOI: 10.1093/neuonc/noy023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Monika E Hegi
- Department of Clinical Neurosciences, Lausanne University Hospital, Lausanne, Switzerland
| | - Paul Kleihues
- Medical Faculty, University of Zürich, Zürich, Switzerland
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Mario L Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Broad Institute of Harvard and MIT, Boston, Massachusetts, USA
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707
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Pérez RF, Santamarina P, Tejedor JR, Urdinguio RG, Álvarez-Pitti J, Redon P, Fernández AF, Fraga MF, Lurbe E. Longitudinal genome-wide DNA methylation analysis uncovers persistent early-life DNA methylation changes. J Transl Med 2019; 17:15. [PMID: 30626398 PMCID: PMC6327427 DOI: 10.1186/s12967-018-1751-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 01/08/2023] Open
Abstract
Background Early life is a period of drastic epigenetic remodeling in which the epigenome is especially sensitive to extrinsic and intrinsic influence. However, the epigenome-wide dynamics of the DNA methylation changes that occur during this period have not been sufficiently characterized in longitudinal studies. Methods To this end, we studied the DNA methylation status of more than 750,000 CpG sites using Illumina MethylationEPIC arrays on 33 paired blood samples from 11 subjects at birth and at 5 and 10 years of age, then characterized the chromatin context associated with these loci by integrating our data with histone, chromatin-state and enhancer-element external datasets, and, finally, validated our results through bisulfite pyrosequencing in two independent longitudinal cohorts of 18 additional subjects. Results We found abundant DNA methylation changes (110,726 CpG sites) during the first lustrum of life, while far fewer alterations were observed in the subsequent 5 years (460 CpG sites). However, our analysis revealed persistent DNA methylation changes at 240 CpG sites, indicating that there are genomic locations of considerable epigenetic change beyond immediate birth. The chromatin context of hypermethylation changes was associated with repressive genomic locations and genes with developmental and cell signaling functions, while hypomethylation changes were linked to enhancer regions and genes with immunological and mRNA and protein metabolism functions. Significantly, our results show that genes that suffer simultaneous hyper- and hypomethylation are functionally distinct from exclusively hyper- or hypomethylated genes, and that enhancer-associated methylation is different in hyper- and hypomethylation scenarios, with hypomethylation being more associated to epigenetic changes at blood tissue-specific enhancer elements. Conclusions These data show that epigenetic remodeling is dramatically reduced after the first 5 years of life. However, there are certain loci which continue to manifest DNA methylation changes, pointing towards a possible functionality beyond early development. Furthermore, our results deepen the understanding of the genomic context associated to hyper- or hypomethylation alterations during time, suggesting that hypomethylation of blood tissue-specific enhancer elements could be of importance in the establishment of functional states in blood tissue during early-life. Electronic supplementary material The online version of this article (10.1186/s12967-018-1751-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Raúl F Pérez
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain.,Nanomedicine Group, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, 33940, Oviedo, Asturias, Spain
| | - Pablo Santamarina
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain.,Nanomedicine Group, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, 33940, Oviedo, Asturias, Spain
| | - Juan Ramón Tejedor
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Rocío G Urdinguio
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Julio Álvarez-Pitti
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, 46014, Valencia, Spain.,Centros de Investigación Biomédica en Red de Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain
| | - Pau Redon
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, 46014, Valencia, Spain.,Centros de Investigación Biomédica en Red de Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain
| | - Agustín F Fernández
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Mario F Fraga
- Nanomedicine Group, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, 33940, Oviedo, Asturias, Spain.
| | - Empar Lurbe
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, 46014, Valencia, Spain. .,Centros de Investigación Biomédica en Red de Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain.
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708
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Wang XM, Tian FY, Fan LJ, Xie CB, Niu ZZ, Chen WQ. Comparison of DNA methylation profiles associated with spontaneous preterm birth in placenta and cord blood. BMC Med Genomics 2019; 12:1. [PMID: 30606219 PMCID: PMC6318854 DOI: 10.1186/s12920-018-0466-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/21/2018] [Indexed: 11/13/2022] Open
Abstract
Background The etiology and mechanism of spontaneous preterm birth (sPTB) are still unclear. Accumulating evidence has documented that various environmental exposure scenarios may cause maternal and fetal epigenetic changes, which initiates the focus on whether epigenetics can contribute to the occurrence of sPTB. Therefore, we conducted the current study to examine and compare the DNA methylation changes associated with sPTB in placenta and cord blood. Methods This hospital-based case-control study was carried out at three Women and Children’s hospitals in South China, where 32 spontaneous preterm births and 16 term births were recruited. Genome-wide DNA methylation profiles of the placenta and cord blood from these subjects were measured using the Illumina HumanMethylation EPIC BeadChip, and sPTB-associated differential methylated CpG sites were identified using limma regression model, after controlling for major maternal and infant confounders. Further Gene Ontology analysis was performed with PANTHER in order to assess different functional enrichment of the sPTB-associated genes in placenta and cord blood. Results After controlling for potential confounding factors, one differentially methylated position (DMP) in placenta and 31 DMPs in cord blood were found significantly associated with sPTB (Bonferroni corrected p < 0.05). The sPTB-associated CpG sites in placenta were mapped to genes that showed higher enrichment on biological processes including biological regulation, multicellular organismal process, and especially response to stimulus, while those in cord blood were mapped to genes that had higher enrichment on biological processes concerning cellular process, localization, and particularly metabolic process. Conclusion Findings of this study indicated that DNA methylation alteration in both placenta and cord blood are associated with sPTB, yet the DNA methylation modification patterns may appear differently in placenta and cord blood. Electronic supplementary material The online version of this article (10.1186/s12920-018-0466-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xi-Meng Wang
- Department of Medical Statistics and Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Assessment, Guangdong Provincial Key Laboratory of Food, Nutrition and Health. School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Fu-Ying Tian
- Department of Medical Statistics and Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Assessment, Guangdong Provincial Key Laboratory of Food, Nutrition and Health. School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China.,Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Li-Jun Fan
- Department of Medical Statistics and Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Assessment, Guangdong Provincial Key Laboratory of Food, Nutrition and Health. School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Chuan-Bo Xie
- Department of Cancer Prevention Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, No 21 Qingcaigang, Jianshe Road 6, Guangzhou, 510600, Guangdong, China
| | - Zhong-Zheng Niu
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, State University of New York at Buffalo, 265 Farber Hall, Buffalo, NY, 14214, USA
| | - Wei-Qing Chen
- Department of Medical Statistics and Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Assessment, Guangdong Provincial Key Laboratory of Food, Nutrition and Health. School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China. .,Department of Information Management, Xinhua College, Sun Yat-sen University, Guangzhou, Guangdong, China.
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709
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Abstract
The characterization of aberrant DNA methylation is emerging as a key part of the study of cancer development and phenotype. The technical advancements and decreasing costs of methods for high-throughput profiling of DNA methylation have brought about a high interest in the use of such methods in disease association studies. Here we discuss the principles for DNA methylation analysis using data from the Infinium DNA methylation BeadChip assays and describe the computational steps and statistical considerations going from processing of the raw array data to analysis of differential methylation. Moreover, we provide detailed guidelines on how to perform tumor subtype classification based on DNA methylation signatures.
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710
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Alekseenko IV, Monastyrskaya GS, Sverdlov ED. Emerging Potential of Cancer Therapy—Binary Direct Interactions of Cancer and Stromal Cells. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418120025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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711
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Mitteldorf J. A Clinical Trial Using Methylation Age to Evaluate Current Antiaging Practices. Rejuvenation Res 2018; 22:201-209. [PMID: 30345885 DOI: 10.1089/rej.2018.2083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent advances in the technology of "aging clocks" based on DNA methylation suggest that it may be possible to measure changes in the rate of human aging over periods as short as a year or two. To the extent that methylation (and other biomarkers) are valid surrogates for biological age, the testing of antiaging interventions has thus become radically cheaper, faster, and more practical. Together with colleagues at UCLA, I have initiated a clinical trial to evaluate some of the most popular antiaging strategies currently deployed by "early adopters" in the lay community of personal health activists. We are recruiting 5000 subjects, age 45-65, and interviewing them in detail about their diet, drugs and supplements, exercise, social, and other practices that plausibly contribute to modulate the rate of aging. They agree to submit blood samples for analysis of methylation age at the beginning, middle, and end of a 2-year test period. Primary endpoint is the difference in methylation age over the course of 2 years. We are in the process of developing a specialized clock, optimized for individual differences over time. Results will be viewed as an exploratory study to identify synergistic combinations of age-retarding treatments. It is our expectation that there is a great deal of redundancy in the strategies that have been researched and promoted to the aware public; thus, most combinations can retard the rate of aging by only a few percent, consistent with the best known single measures. However, we hope that among the many strategies that our subjects have adopted, there will be some combinations that synergize and achieve age retardation by ≥25% or more. A mock-up analysis of computer-generated data has been performed to fix parameters of the study, and confirm that such combinations will be able to be detected with good probability, should they exist. All data (redacted for privacy) will be open sourced, available to the scientific community and to the public.
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Affiliation(s)
- Josh Mitteldorf
- 1 School of Medicine, Washington University in St Louis, St Louis, Missouri.,2 National Institute of Biological Sciences, Beijing, China
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712
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Huen K, Solomon O, Kogut K, Eskenazi B, Holland N. PON1 DNA methylation and neurobehavior in Mexican-American children with prenatal organophosphate exposure. ENVIRONMENT INTERNATIONAL 2018; 121:31-40. [PMID: 30172926 PMCID: PMC6242297 DOI: 10.1016/j.envint.2018.08.044] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/17/2018] [Accepted: 08/18/2018] [Indexed: 06/08/2023]
Abstract
PON1 is a multifunctional enzyme involved in oxidative stress and detoxification of some organophosphate (OP) pesticides. It has been associated with nervous system diseases like Alzheimer's disease, amyotrophic lateral sclerosis, Parkinson's disease, and autism. We previously found that PON1 susceptible genotypes were associated with lower IQ scores in children. Epigenetic marks, such as DNA methylation, can regulate gene expression. Yet, data on whether DNA methylation may influence the relationship between PON1 levels and neurobehavior are limited. In this study, we used Illumina 450K and EPIC BeadChip arrays to assess PON1 DNA methylation in blood specimens collected from children (n = 238) at birth (cord blood) and age 7 years and examined their relationship with cognitive outcomes. The Wechsler Intelligence Scale for Children was used to assess Full Scale IQ and four composite measures (Verbal Comprehension, Perceptual Reasoning, Working Memory, and Processing Speed Indexes) in 7-year-old children. We observed a consistent yet nonsignificant inverse relationship of methylation at several CpG sites close to the PON1 transcription start site with Full Scale IQ and other composite measures of cognition. We also found an inverse relationship between cord blood methylation at cg15887283 with working memory and a positive association of 7-year-old methylation at cg22798737 with processing speed, independent of OP exposure. However, none of the associations remained significant after accounting for multiple comparisons. This study provides some evidence of the role DNA methylation may play in the known relationship between PON1 and neurobehavior in children, however it appears to be only suggestive and warrants additional research.
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Affiliation(s)
- Karen Huen
- Children's Environmental Health Laboratory, Global Berkeley Campus, 1301 S. 46th Street, Bldg 112, Richmond, CA 94804, USA.
| | - Olivia Solomon
- Children's Environmental Health Laboratory, Global Berkeley Campus, 1301 S. 46th Street, Bldg 112, Richmond, CA 94804, USA
| | - Katherine Kogut
- Center for Children's Environmental Health, School of Public Health, University of California, Berkeley, 1995 University Avenue Suite 265, Berkeley, CA 94720, USA
| | - Brenda Eskenazi
- Center for Children's Environmental Health, School of Public Health, University of California, Berkeley, 1995 University Avenue Suite 265, Berkeley, CA 94720, USA
| | - Nina Holland
- Children's Environmental Health Laboratory, Global Berkeley Campus, 1301 S. 46th Street, Bldg 112, Richmond, CA 94804, USA
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713
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Bearer EL, Mulligan BS. Epigenetic Changes Associated with Early Life Experiences: Saliva, A Biospecimen for DNA Methylation Signatures. Curr Genomics 2018; 19:676-698. [PMID: 30532647 PMCID: PMC6225450 DOI: 10.2174/1389202919666180307150508] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 08/21/2017] [Accepted: 03/04/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Adverse Childhood Experiences (ACEs), which include traumatic injury, are associated with poor health outcomes in later life, yet the biological mechanisms mediating this association are unknown. Neurocircuitry, immune system and hormone regulation differ from normal in adults reporting ACEs. These systems could be affected by epigenetic changes, including methylation of cytosine (5mC) in genomic DNA, activated by ACEs. Since 5mC levels influence gene expression and can be long-lasting, altered 5mC status at specific sites or throughout the genome is hypothesized to influence mental and physical outcomes after ACE(s). Human and animal studies support this, with animal models allowing experiments for attributing causality. Here we provide a lengthy introduction and background on 5mC and the impact of early life adversity. OBJECTIVE Next we address the issue of a mixture of cell types in saliva, the most accessible biospecimen for 5mC analysis. Typical human bio-specimens for 5mC analysis include saliva or buccal swabs, whole blood or types of blood cells, tumors and post-mortem brain. In children saliva is the most accessible biospecimen, but contains a mixture of keratinocytes and white blood cells, as do buccal swabs. Even in saliva from the same individual at different time points, cell composition may differ widely. Similar issues affect analysis in blood, where nucleated cells represent a wide array of white blood cell types. Unless variations in ratios of these cells between each sample are included in the analysis, results can be unreliable. METHODS Several different biochemical assays are available to test for site-specific methylation levels genome-wide, each producing different information, with high-density arrays being the easiest to use, and bisulfite whole genome sequencing the most comprehensive. We compare results from different assays and use high-throughput computational processing to deconvolve cell composition in saliva samples. RESULTS Here we present examples demonstrating the critical importance of determining the relative contribution of blood cells versus keratinocytes to the 5mC profile found in saliva. We further describe a strategy to perform a reference-based computational correction for cell composition, and therefore to identify differential methylation patterns due to experience, or for the diagnosis of phenotypes that correlate between traits, such as hormone levels, trauma status and various mental health outcomes. CONCLUSION Specific sites that respond to adversity with altered methylation levels in either blood cells, keratinocytes or both can be identified by this rigorous approach, which will then be useful as diagnostic biomarkers and therapeutic targets.
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Affiliation(s)
- Elaine L. Bearer
- Address correspondence to this author at the Department of Pathology MSC 08-4640, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131, USA; Tel: 505-272-2404; Fax: 505-272-8084; E-mails: ;
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714
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James P, Sajjadi S, Tomar AS, Saffari A, Fall CHD, Prentice AM, Shrestha S, Issarapu P, Yadav DK, Kaur L, Lillycrop K, Silver M, Chandak GR. Candidate genes linking maternal nutrient exposure to offspring health via DNA methylation: a review of existing evidence in humans with specific focus on one-carbon metabolism. Int J Epidemiol 2018; 47:1910-1937. [PMID: 30137462 PMCID: PMC6280938 DOI: 10.1093/ije/dyy153] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2018] [Indexed: 12/13/2022] Open
Abstract
Background Mounting evidence suggests that nutritional exposures during pregnancy influence the fetal epigenome, and that these epigenetic changes can persist postnatally, with implications for disease risk across the life course. Methods We review human intergenerational studies using a three-part search strategy. Search 1 investigates associations between preconceptional or pregnancy nutritional exposures, focusing on one-carbon metabolism, and offspring DNA methylation. Search 2 considers associations between offspring DNA methylation at genes found in the first search and growth-related, cardiometabolic and cognitive outcomes. Search 3 isolates those studies explicitly linking maternal nutritional exposure to offspring phenotype via DNA methylation. Finally, we compile all candidate genes and regions of interest identified in the searches and describe their genomic locations, annotations and coverage on the Illumina Infinium Methylation beadchip arrays. Results We summarize findings from the 34 studies found in the first search, the 31 studies found in the second search and the eight studies found in the third search. We provide details of all regions of interest within 45 genes captured by this review. Conclusions Many studies have investigated imprinted genes as priority loci, but with the adoption of microarray-based platforms other candidate genes and gene classes are now emerging. Despite a wealth of information, the current literature is characterized by heterogeneous exposures and outcomes, and mostly comprise observational associations that are frequently underpowered. The synthesis of current knowledge provided by this review identifies research needs on the pathway to developing possible early life interventions to optimize lifelong health.
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Affiliation(s)
- Philip James
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Sara Sajjadi
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Ashutosh Singh Tomar
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Ayden Saffari
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Caroline H D Fall
- MRC Life course Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Andrew M Prentice
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Smeeta Shrestha
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- School of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, India
| | - Prachand Issarapu
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Dilip Kumar Yadav
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Lovejeet Kaur
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Karen Lillycrop
- Research Centre for Biological Sciences, Institute of Developmental Sciences, University of Southampton, Southampton, UK
| | - Matt Silver
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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715
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Moss J, Magenheim J, Neiman D, Zemmour H, Loyfer N, Korach A, Samet Y, Maoz M, Druid H, Arner P, Fu KY, Kiss E, Spalding KL, Landesberg G, Zick A, Grinshpun A, Shapiro AMJ, Grompe M, Wittenberg AD, Glaser B, Shemer R, Kaplan T, Dor Y. Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nat Commun 2018; 9:5068. [PMID: 30498206 PMCID: PMC6265251 DOI: 10.1038/s41467-018-07466-6] [Citation(s) in RCA: 522] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/05/2018] [Indexed: 01/12/2023] Open
Abstract
Methylation patterns of circulating cell-free DNA (cfDNA) contain rich information about recent cell death events in the body. Here, we present an approach for unbiased determination of the tissue origins of cfDNA, using a reference methylation atlas of 25 human tissues and cell types. The method is validated using in silico simulations as well as in vitro mixes of DNA from different tissue sources at known proportions. We show that plasma cfDNA of healthy donors originates from white blood cells (55%), erythrocyte progenitors (30%), vascular endothelial cells (10%) and hepatocytes (1%). Deconvolution of cfDNA from patients reveals tissue contributions that agree with clinical findings in sepsis, islet transplantation, cancer of the colon, lung, breast and prostate, and cancer of unknown primary. We propose a procedure which can be easily adapted to study the cellular contributors to cfDNA in many settings, opening a broad window into healthy and pathologic human tissue dynamics. The methylation status of circulating cell-free DNA (cfDNA) can be informative about recent cell death events. Here the authors present an approach to determine the tissue origins of cfDNA, using a reference methylation atlas of 25 human tissues and cell types, and find that cfDNA from patients reveals tissue contributions that agree with clinical findings.
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Affiliation(s)
- Joshua Moss
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel.,School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Judith Magenheim
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Daniel Neiman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Hai Zemmour
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Amit Korach
- Department of Cardio-Thoracic Surgery, Hadassah-Hebrew University Medical Center, Jerusalem, 9112001, Israel
| | - Yaacov Samet
- Department of Vascular Surgery, Hadassah-Hebrew University Medical Center, Jerusalem, 9112001, Israel
| | - Myriam Maoz
- Department of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, 9112001, Israel
| | - Henrik Druid
- Department of Oncology-Pathology, Karolinska Institutet, SE17177, Stockholm, Sweden.,Dept of Forensic Medicine, The National Board of Forensic Medicine, SE11120, Stockholm, Sweden
| | - Peter Arner
- Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE17176, Stockholm, Sweden
| | - Keng-Yeh Fu
- Department of Cell and Molecular Biology, Karolinska Institutet, SE17177, Stockholm, Sweden
| | - Endre Kiss
- Department of Cell and Molecular Biology, Karolinska Institutet, SE17177, Stockholm, Sweden
| | - Kirsty L Spalding
- Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE17176, Stockholm, Sweden.,Department of Cell and Molecular Biology, Karolinska Institutet, SE17177, Stockholm, Sweden
| | - Giora Landesberg
- Dept of Anesthesiology and Critical Care Medicine, Hadassah-Hebrew University Medical Center, 9112001, Jerusalem, Israel
| | - Aviad Zick
- Department of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, 9112001, Israel
| | - Albert Grinshpun
- Department of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, 9112001, Israel
| | - A M James Shapiro
- Department of Surgery and the Clinical Islet Transplant Program, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Markus Grompe
- Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Avigail Dreazan Wittenberg
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Benjamin Glaser
- Dept of Endocrinology and Metabolism Service, Hadassah-Hebrew University Medical Center, 9112001, Jerusalem, Israel
| | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel.
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel.
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716
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Hannon E, Gorrie-Stone TJ, Smart MC, Burrage J, Hughes A, Bao Y, Kumari M, Schalkwyk LC, Mill J. Leveraging DNA-Methylation Quantitative-Trait Loci to Characterize the Relationship between Methylomic Variation, Gene Expression, and Complex Traits. Am J Hum Genet 2018; 103:654-665. [PMID: 30401456 PMCID: PMC6217758 DOI: 10.1016/j.ajhg.2018.09.007] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/14/2018] [Indexed: 11/23/2022] Open
Abstract
Characterizing the complex relationship between genetic, epigenetic, and transcriptomic variation has the potential to increase understanding about the mechanisms underpinning health and disease phenotypes. We undertook a comprehensive analysis of common genetic variation on DNA methylation (DNAm) by using the Illumina EPIC array to profile samples from the UK Household Longitudinal study. We identified 12,689,548 significant DNA methylation quantitative trait loci (mQTL) associations (p < 6.52 × 10-14) occurring between 2,907,234 genetic variants and 93,268 DNAm sites, including a large number not identified by previous DNAm-profiling methods. We demonstrate the utility of these data for interpreting the functional consequences of common genetic variation associated with > 60 human traits by using summary-data-based Mendelian randomization (SMR) to identify 1,662 pleiotropic associations between 36 complex traits and 1,246 DNAm sites. We also use SMR to characterize the relationship between DNAm and gene expression and thereby identify 6,798 pleiotropic associations between 5,420 DNAm sites and the transcription of 1,702 genes. Our mQTL database and SMR results are available via a searchable online database as a resource to the research community.
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Affiliation(s)
- Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
| | - Tyler J Gorrie-Stone
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Melissa C Smart
- Institute for Social and Economic Research, University of Essex, Colchester CO3 3LG, United Kingdom
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
| | - Amanda Hughes
- Institute for Social and Economic Research, University of Essex, Colchester CO3 3LG, United Kingdom
| | - Yanchun Bao
- Institute for Social and Economic Research, University of Essex, Colchester CO3 3LG, United Kingdom
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester CO3 3LG, United Kingdom
| | - Leonard C Schalkwyk
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom.
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717
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Methylome of human skeletal muscle after acute & chronic resistance exercise training, detraining & retraining. Sci Data 2018; 5:180213. [PMID: 30375987 PMCID: PMC6207066 DOI: 10.1038/sdata.2018.213] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/22/2018] [Indexed: 01/08/2023] Open
Abstract
DNA methylation is an important epigenetic modification that can regulate gene expression following environmental encounters without changes to the genetic code. Using Infinium MethylationEPIC BeadChip Arrays (850,000 CpG sites) we analysed for the first time, DNA isolated from untrained human skeletal muscle biopsies (vastus lateralis) at baseline (rest) and immediately following an acute (single) bout of resistance exercise. In the same participants, we also analysed the methylome following a period of muscle growth (hypertrophy) evoked via chronic (repeated bouts-3 sessions/wk) resistance exercise (RE) (training) over 7-weeks, followed by complete exercise cessation for 7-weeks returning muscle back to baseline levels (detraining), and finally followed by a subsequent 7-week period of RE-induced hypertrophy (retraining). These valuable methylome data sets described in the present manuscript and deposited in an open-access repository can now be shared and re-used to enable the identification of epigenetically regulated genes/networks that are modified after acute anabolic stimuli and hypertrophy, and further investigate the phenomenon of epigenetic memory in skeletal muscle.
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718
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Smyth LJ, Maxwell AP, Benson KA, Kilner J, McKay GJ, McKnight AJ. Validation of differentially methylated microRNAs identified from an epigenome-wide association study; Sanger and next generation sequencing approaches. BMC Res Notes 2018; 11:767. [PMID: 30373632 PMCID: PMC6206874 DOI: 10.1186/s13104-018-3872-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/22/2018] [Indexed: 12/21/2022] Open
Abstract
Objectives Altered DNA methylation and microRNA profiles are associated with diabetic kidney disease. This study compared different sequencing approaches to define the genetic and epigenetic architecture of sequences surrounding microRNAs associated with diabetic kidney disease. Results We compared Sanger and next generation sequencing to validate microRNAs associated with diabetic kidney disease identified from an epigenome-wide association study (EWAS). These microRNAs demonstrated differential methylation levels in cases with diabetic kidney disease compared to controls with long duration of type 1 diabetes and no evidence of kidney disease (Padjusted < 10−5). Targeted next generation sequencing analysis of genomic DNA and matched cell-line transformed DNA samples identified four genomic variants within the microRNAs, two within miR-329-2 and two within miR-429. Sanger sequencing of genomic DNA replicated these findings and confirmed the altered methylation status of the CpG sites identified by the EWAS in bisulphite-treated DNA. This investigation successfully fine-mapped the genetic sequence around key microRNAs. Variants have been detected which may affect their methylation status and methylated CpG sites have been confirmed. Additionally, we explored both the fidelity of next generation sequencing analysis and the potential efficacy of cell-line transformed DNA samples in place of finite patient samples in discovery genetic and epigenetic research. Electronic supplementary material The online version of this article (10.1186/s13104-018-3872-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laura J Smyth
- Genetic Epidemiology Research Group, Centre for Public Health, Queen's University of Belfast, Belfast, UK.
| | - Alexander P Maxwell
- Genetic Epidemiology Research Group, Centre for Public Health, Queen's University of Belfast, Belfast, UK
| | - Katherine A Benson
- Genetic Epidemiology Research Group, Centre for Public Health, Queen's University of Belfast, Belfast, UK
| | - Jill Kilner
- Genetic Epidemiology Research Group, Centre for Public Health, Queen's University of Belfast, Belfast, UK
| | - Gareth J McKay
- Genetic Epidemiology Research Group, Centre for Public Health, Queen's University of Belfast, Belfast, UK
| | - Amy Jayne McKnight
- Genetic Epidemiology Research Group, Centre for Public Health, Queen's University of Belfast, Belfast, UK
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719
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Konwar C, Price EM, Wang LQ, Wilson SL, Terry J, Robinson WP. DNA methylation profiling of acute chorioamnionitis-associated placentas and fetal membranes: insights into epigenetic variation in spontaneous preterm births. Epigenetics Chromatin 2018; 11:63. [PMID: 30373633 PMCID: PMC6205793 DOI: 10.1186/s13072-018-0234-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/20/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Placental inflammation, often presenting as acute chorioamnionitis (aCA), is commonly associated with preterm birth. Preterm birth can have both immediate and long-term adverse effects on the health of the baby. Developing biomarkers of inflammation in the placenta can help to understand its effects and potentially lead to new approaches for rapid prenatal diagnosis of aCA. We aimed to characterize epigenetic variation associated with aCA in placenta (chorionic villi) and fetal membranes (chorion and amnion) to better understand how aCA may impact processes that lead to preterm birth. This study lays the groundwork for development of novel biomarkers for aCA. METHODS Samples from 44 preterm placentas (chorionic villi) as well as matched chorion and amnion for 16 of these cases were collected for this study. These samples were profiled using the Illumina Infinium HumanMethylation850 BeadChip to measure DNA methylation (DNAm) at 866,895 CpGs across the genome. An additional 78 placental samples were utilized to independently validate the array findings by pyrosequencing. RESULTS Using a false discovery rate of < 0.15 and average group difference in DNAm of > 0.05, 66 differentially methylated (DM) CpG sites were identified between aCA cases and non-aCA cases in chorionic villi. For the majority of these 66 DM CpGs, the DNAm profile of the aCA cases as compared to the non-aCA cases trended in the direction of the blood cell DNAm. Interestingly, neutrophil-specific DNAm signatures, but not those associated with other immune cell types, were capable of separating aCA cases from the non-aCA cases. CONCLUSIONS Our results suggest that aCA-associated placentas showed altered DNAm signatures that were not observed in the absence of aCA. This DNAm profile is consistent with the activation of the innate immune response in the placenta and/or reflect increase in neutrophils as a response to inflammation.
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Affiliation(s)
- Chaini Konwar
- BC Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1 Canada
| | - E. Magda Price
- BC Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1 Canada
- Department of Pediatrics, University of British Columbia, Vancouver, BC V6H 3N1 Canada
| | - Li Qing Wang
- BC Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada
- University of British Columbia, Vancouver, BC V6H 3N1 Canada
| | - Samantha L. Wilson
- BC Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1 Canada
| | - Jefferson Terry
- BC Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada
- Department of Pathology, BC Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | - Wendy P. Robinson
- BC Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1 Canada
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720
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Zaimi I, Pei D, Koestler DC, Marsit CJ, De Vivo I, Tworoger SS, Shields AE, Kelsey KT, Michaud DS. Variation in DNA methylation of human blood over a 1-year period using the Illumina MethylationEPIC array. Epigenetics 2018; 13:1056-1071. [PMID: 30270718 PMCID: PMC6342169 DOI: 10.1080/15592294.2018.1530008] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 08/02/2018] [Accepted: 09/22/2018] [Indexed: 12/29/2022] Open
Abstract
Assessing DNA methylation profiles in human blood has become a major focus of epidemiologic inquiry. Understanding variability in CpG-specific DNA methylation over moderate periods of time is a critical first step in identifying CpG sites that are candidates for DNA methylation-based etiologic, diagnostic and prognostic predictors of pathogenesis. Using the Illumina MethylationEPIC [850K] BeadArray, DNA methylation was profiled in paired whole blood samples collected approximately 1 year apart from 35 healthy women enrolled in the Nurses Study II cohort. The median intraclass correlation coefficient (ICC) across all CpG loci was 0.19 [Interquartile Range (IQR) 0.00-0.50]; 74.8% of ICCs were in the low range (0-0.5), 16.9% in the mid-range of ICCs (0.5-0.8), and 8.3% in the high-range of ICCs (0.8-1). ICCs were similar for CpG probes on the 450K Illumina array (median 0.17) and the new probes added to the 850K array (median 0.21). ICCs for CpG loci on the sex chromosomes and known metastable epialleles were high (median 0.71, 0.97, respectively), and ICCs among methylation quantitative trait loci (mQTL) CpGs were significantly higher as compared to non-mQTL CpGs (median 0.73, 0.16, respectively, P < 2 × 10-16). We observed wide variation in DNA methylation stability over a 1-year period. Probes considered non-stable, due to substantial variation over a moderate period of time and with minimal variability across individuals could be removed in large epidemiological studies. Moreover, adjusting for technical variation that arises from using high-dimensional arrays is critical.
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Affiliation(s)
- Ina Zaimi
- a Department of Public Health & Community Medicine, Tufts University School of Medicine , Tufts University , Boston , USA
| | - Dong Pei
- b Department of Biostatistics , University of Kansas Medical Center , Kansas City , USA
- c University of Kansas Cancer Center , The University of Kansas Medical Center , Kansas City , USA
| | - Devin C Koestler
- b Department of Biostatistics , University of Kansas Medical Center , Kansas City , USA
- c University of Kansas Cancer Center , The University of Kansas Medical Center , Kansas City , USA
| | - Carmen J Marsit
- d Department of Environmental Health and Department of Epidemiology, Rollins School of Public Health , Emory University , Atlanta , USA
| | - Immaculata De Vivo
- e Channing Division of Network Medicine, Department of Medicine , Brigham and Women's Hospital and Harvard Medical School , Boston , USA
| | - Shelley S Tworoger
- f Department of Cancer Epidemiology , Moffitt Cancer Center , Tampa , USA
- g Department of Epidemiology , Harvard T.H. Chan School of Public Health , Boston , USA
| | - Alexandra E Shields
- h Department of Medicine , Harvard Medical School , Boston , MA , USA
- k Harvard/MGH Center on Genomics, Vulnerable Populations, and Health Disparities , Massachusetts General Hospital , Boston , MA , USA
| | - Karl T Kelsey
- i Department of Epidemiology , Brown University , Providence , USA
- j Department of Pathology and Laboratory Medicine , Brown University , Providence , USA
| | - Dominique S Michaud
- a Department of Public Health & Community Medicine, Tufts University School of Medicine , Tufts University , Boston , USA
- i Department of Epidemiology , Brown University , Providence , USA
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721
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Ambatipudi S, Langdon R, Richmond RC, Suderman M, Koestler DC, Kelsey KT, Kazmi N, Penfold C, Ho KM, McArdle W, Ring SM, Pring M, Waterboer T, Pawlita M, Gaunt TR, Davey Smith G, Thomas S, Ness AR, Relton CL. DNA methylation derived systemic inflammation indices are associated with head and neck cancer development and survival. Oral Oncol 2018; 85:87-94. [PMID: 30220325 PMCID: PMC6156796 DOI: 10.1016/j.oraloncology.2018.08.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/31/2018] [Accepted: 08/26/2018] [Indexed: 12/18/2022]
Abstract
OBJECTIVES Head and neck squamous cell carcinoma (HNSCC) is often associated with chronic systemic inflammation (SI). In the present study, we assessed if DNA methylation-derived SI (mdSI) indices: Neutrophil-to-Lymphocyte ratio (mdNLR) and Lymphocyte-to-Monocyte ratio (mdLMR) are associated with the presence of HNSCC and overall survival (OS). MATERIALS AND METHODS We used two peripheral blood DNA methylation datasets: an HNSCC case-control dataset (n = 183) and an HNSCC survival dataset (n = 407) to estimate mdSI indices. We then performed multivariate regressions to test the association between mdSI indices, HNSCC development and OS. RESULTS Multivariate logistic regression revealed that elevated mdNLR was associated with increased odds of being an HNSCC case (OR = 3.25, 95% CI = 2.14-5.34, P = 4 × 10-7) while the converse was observed for mdLMR (OR = 0.88, 95% CI = 0.81-0.90, P = 2 × 10-3). In the HNSCC survival dataset, HPV16-E6 seropositive HNSCC cases had an elevated mdLMR (P = 9 × 10-5) and a lower mdNLR (P = 0.003) compared to seronegative patients. Multivariate Cox regression in the HNSCC survival dataset revealed that lower mdLMR (HR = 1.96, 95% CI = 1.30-2.95, P = 0.0013) but not lower mdNLR (HR = 0.68, 95% CI = 0.46-1.00, P = 0.0501) was associated with increased risk of death. CONCLUSION Our results indicate that mdSI estimated by DNA methylation data is associated with the presence of HNSCC and overall survival. The mdSI indices may be used as a valuable research tool to reliably estimate SI in the absence of cell-based estimates. Rigorous validation of our findings in large prospective studies is warranted in the future.
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Affiliation(s)
- Srikant Ambatipudi
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Ryan Langdon
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, School of Public Health, Providence, RI 02912, USA; Department of Laboratory Medicine & Pathology, Brown University, Providence, RI 02912, USA
| | - Nabila Kazmi
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Christopher Penfold
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol NHS Foundation Trust and University of Bristol, Bristol, UK
| | - Karen M Ho
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Wendy McArdle
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Susan M Ring
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Miranda Pring
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol NHS Foundation Trust and University of Bristol, Bristol, UK
| | - Tim Waterboer
- Division of Molecular Diagnostics of Oncogenic Infections, Infection, Inflammation and Cancer Program, German Cancer Research Center, Heidelberg, Germany
| | - Michael Pawlita
- Division of Molecular Diagnostics of Oncogenic Infections, Infection, Inflammation and Cancer Program, German Cancer Research Center, Heidelberg, Germany
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Steve Thomas
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol NHS Foundation Trust and University of Bristol, Bristol, UK
| | - Andy R Ness
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol NHS Foundation Trust and University of Bristol, Bristol, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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722
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Moon DH, Kwon SO, Kim WJ, Hong Y. Identification of Serial DNA Methylation Changes in the Blood Samples of Patients with Lung Cancer. Tuberc Respir Dis (Seoul) 2018; 82:126-132. [PMID: 30302959 PMCID: PMC6435926 DOI: 10.4046/trd.2018.0042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 06/21/2018] [Accepted: 07/31/2018] [Indexed: 12/21/2022] Open
Abstract
Background The development of lung cancer results from the interaction between genetic mutations and dynamic epigenetic alterations, although the exact mechanisms are not completely understood. Changes in DNA methylation may be a promising biomarker for early detection and prognosis of lung cancer. We evaluated the serial changes in genome-wide DNA methylation patterns in blood samples of lung cancer patients. Methods Blood samples were obtained for three consecutive years from three patients (2 years before, 1 year before, and after lung cancer detection) and from three control subjects (without lung cancer). We used the MethylationEPIC BeadChip method, which covers the 850,000 bp cytosine-phosphate-guanine (CpG) site, to conduct an epigenome-wide analysis. Significant differentially methylated regions (DMRs) were identified using p-values <0.05 in a correlation test identifying serial methylation changes and serial increase or decrease in β value above 0.1 for three consecutive years. Results We found three significant CpG sites with differentially methylated β values and 7,105 CpG sites with significant correlation from control patients without lung cancer. However, there were no significant DMRs. In contrast, we found 11 significant CpG sites with differentially methylated β values and 10,562 CpG sites with significant correlation from patients with lung cancer. There were two significant DMRs: cg21126229 (RNF212) and cg27098574 (BCAR1). Conclusion This study revealed DNA methylation changes that might be implicated in lung cancer development. The DNA methylation changes may be the possible candidate target regions for the early detection and prevention of lung cancer.
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Affiliation(s)
- Da Hye Moon
- Department of Internal Medicine, Kangwon National University Hospital, Chuncheon, Korea
| | - Sung Ok Kwon
- Biomedical Research Institute, Kangwon National University Hospital, Chuncheon, Korea
| | - Woo Jin Kim
- Department of Internal Medicine, Kangwon National University Hospital, Chuncheon, Korea.,Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
| | - Yoonki Hong
- Department of Internal Medicine, Kangwon National University Hospital, Chuncheon, Korea.,Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Korea.
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723
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van Dongen J, Ehli EA, Jansen R, van Beijsterveldt CEM, Willemsen G, Hottenga JJ, Kallsen NA, Peyton SA, Breeze CE, Kluft C, Heijmans BT, Bartels M, Davies GE, Boomsma DI. Genome-wide analysis of DNA methylation in buccal cells: a study of monozygotic twins and mQTLs. Epigenetics Chromatin 2018; 11:54. [PMID: 30253792 PMCID: PMC6156977 DOI: 10.1186/s13072-018-0225-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/17/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND DNA methylation arrays are widely used in epigenome-wide association studies and methylation quantitative trait locus (mQTL) studies. Here, we performed the first genome-wide analysis of monozygotic (MZ) twin correlations and mQTLs on data obtained with the Illumina MethylationEPIC BeadChip (EPIC array) and compared the performance of the EPIC array to the Illumina HumanMethylation450 BeadChip (HM450 array) for buccal-derived DNA. RESULTS Good-quality EPIC data were obtained for 102 buccal-derived DNA samples from 49 MZ twin pairs (mean age = 7.5 years, range = 1-10). Differences between MZ twins in the cellular content of buccal swabs were a major driver for differences in their DNA methylation profiles, highlighting the importance to adjust for cellular composition in DNA methylation studies of buccal-derived DNA. After adjusting for cellular composition, the genome-wide mean correlation (r) between MZ twins was 0.21 for the EPIC array, and cis mQTL analysis in 84 twins identified 1,296,323 significant associations (FDR 5%), encompassing 33,749 methylation sites and 616,029 genetic variants. MZ twin correlations were slightly larger (p < 2.2 × 10-16) for novel EPIC probes (N = 383,066, mean r = 0.22) compared to probes that are also present on HM450 (N = 406,822, mean r = 0.20). In line with this observation, a larger percentage of novel EPIC probes was associated with genetic variants (novel EPIC probes with significant mQTL 4.7%, HM450 probes with mQTL 3.9%, p < 2.2 × 10-16). Methylation sites with a large MZ correlation and sites associated with mQTLs were most strongly enriched in epithelial cell DNase I hypersensitive sites (DHSs), enhancers, and histone mark H3K4me3. CONCLUSIONS We conclude that the contribution of familial factors to individual differences in DNA methylation and the effect of mQTLs are larger for novel EPIC probes, especially those within regulatory elements connected to active regions specific to the investigated tissue.
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Affiliation(s)
- Jenny van Dongen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Erik A. Ehli
- Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, SD 57108 USA
| | - Rick Jansen
- Department of Psychiatry, VU University Medical Center, Oldenaller 1, 1081 HJ Amsterdam, The Netherlands
| | - Catharina E. M. van Beijsterveldt
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Jouke J. Hottenga
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Noah A. Kallsen
- Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, SD 57108 USA
| | - Shanna A. Peyton
- Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, SD 57108 USA
| | - Charles E. Breeze
- Altius Institute for Biomedical Sciences, 2211 Elliott Ave, Seattle, WA 98121 USA
| | - Cornelis Kluft
- Good Biomarker Sciences, Zernikedreef 8, 2333 CL Leiden, The Netherlands
| | - Bastiaan T. Heijmans
- Molecular Epidemiology Section, Leiden University Medical Center, Postal Zone S-05-P, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Meike Bartels
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Gareth E. Davies
- Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, SD 57108 USA
| | - Dorret I. Boomsma
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
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724
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Stevens AJ, Rucklidge JJ, Darling KA, Eggleston MJ, Pearson JF, Kennedy MA. Methylomic changes in response to micronutrient supplementation and MTHFR genotype. Epigenomics 2018; 10:1201-1214. [PMID: 30182732 DOI: 10.2217/epi-2018-0029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Exposure times and dosage required for dietary components to modify DNA methylation patterns are largely unknown. AIM This exploratory research represents the first genome-wide analysis of DNA methylation changes during a randomized-controlled-trial (RCT) for dietary supplementation with broad spectrum vitamins, minerals and amino acids in humans. METHODS Genome-wide changes in methylation from paired, peripheral blood samples were assessed using the Infinium Methylation EPIC 850 K array. RESULTS Methylation increased at 84% of the most significant differentially methylated CpGs; however, none showed significance after adjustment for genome-wide testing. CONCLUSION Micronutrient supplementation is unlikely to have a substantial biological effect on DNA methylation over 10 weeks; however, the trend toward hypermethylation that we observed is likely to become more marked with longer exposure periods.
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Affiliation(s)
- Aaron J Stevens
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, P.O. Box 4345, Christchurch, New Zealand
| | - Julia J Rucklidge
- Department of Psychology, University of Canterbury, Christchurch, New Zealand
| | - Kathryn A Darling
- Department of Psychology, University of Canterbury, Christchurch, New Zealand
| | - Matthew Jf Eggleston
- Department of Psychological Medicine, University of Otago, Christchurch, P.O. Box 4345, Christchurch, New Zealand
| | - John F Pearson
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, P.O. Box 4345, Christchurch, New Zealand
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, P.O. Box 4345, Christchurch, New Zealand
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725
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Solomon O, MacIsaac J, Quach H, Tindula G, Kobor MS, Huen K, Meaney MJ, Eskenazi B, Barcellos LF, Holland N. Comparison of DNA methylation measured by Illumina 450K and EPIC BeadChips in blood of newborns and 14-year-old children. Epigenetics 2018; 13:655-664. [PMID: 30044683 PMCID: PMC6140901 DOI: 10.1080/15592294.2018.1497386] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Analysis of DNA methylation helps to understand the effects of environmental exposures as well as the role of epigenetics in human health. Illumina, Inc. recently replaced the HumanMethylation450 BeadChip (450K) with the EPIC BeadChip, which nearly doubles the measured CpG sites to >850,000. Although the new chip uses the same underlying technology, it is important to establish if data between the two platforms are comparable within cohorts and for meta-analyses. DNA methylation was assessed by 450K and EPIC using whole blood from newborn (n = 109) and 14-year-old (n = 86) participants of the Center for the Health Assessment of Mothers and Children of Salinas. The overall per-sample correlations were very high (r >0.99), although many individual CpG sites, especially those with low variance of methylation, had lower correlations (median r = 0.24). There was also a small subset of CpGs with large mean methylation β-value differences between platforms, in both the newborn and 14-year datasets. However, estimates of cell type proportion prediction by 450K and EPIC were highly correlated at both ages. Finally, differentially methylated positions between boys and girls replicated very well by both platforms in newborns and older children. These findings are encouraging for application of combined data from EPIC and 450K platforms for birth cohorts and other population studies. These data in children corroborate recent comparisons of the two BeadChips in adults and in cancer cell lines. However, researchers should be cautious when characterizing individual CpG sites and consider independent methods for validation of significant hits.
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Affiliation(s)
- Olivia Solomon
- a School of Public Health, Center for Environmental Research and Children's Health (CERCH) , University of California, Berkeley , Berkeley , CA , USA
| | - Julie MacIsaac
- b BC Children's Hospital Research , University of British Columbia , Vancouver , Canada
| | - Hong Quach
- c Genetic Epidemiology and Genomics Laboratory, School of Public Health , University of California, Berkeley , Berkeley , CA , USA
| | - Gwen Tindula
- a School of Public Health, Center for Environmental Research and Children's Health (CERCH) , University of California, Berkeley , Berkeley , CA , USA
| | - Michael S Kobor
- b BC Children's Hospital Research , University of British Columbia , Vancouver , Canada
| | - Karen Huen
- a School of Public Health, Center for Environmental Research and Children's Health (CERCH) , University of California, Berkeley , Berkeley , CA , USA
| | - Michael J Meaney
- d Ludmer Centre for Neuroinformatics & Mental Health, Douglas University Mental Health Research Institute , McGill University , Montreal , Canada
| | - Brenda Eskenazi
- a School of Public Health, Center for Environmental Research and Children's Health (CERCH) , University of California, Berkeley , Berkeley , CA , USA
| | - Lisa F Barcellos
- c Genetic Epidemiology and Genomics Laboratory, School of Public Health , University of California, Berkeley , Berkeley , CA , USA
| | - Nina Holland
- a School of Public Health, Center for Environmental Research and Children's Health (CERCH) , University of California, Berkeley , Berkeley , CA , USA
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726
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Pisanic TR, Cope LM, Lin SF, Yen TT, Athamanolap P, Asaka R, Nakayama K, Fader AN, Wang TH, Shih IM, Wang TL. Methylomic Analysis of Ovarian Cancers Identifies Tumor-Specific Alterations Readily Detectable in Early Precursor Lesions. Clin Cancer Res 2018; 24:6536-6547. [PMID: 30108103 DOI: 10.1158/1078-0432.ccr-18-1199] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/12/2018] [Accepted: 08/09/2018] [Indexed: 12/22/2022]
Abstract
PURPOSE High-grade serous ovarian carcinoma (HGSOC) typically remains undiagnosed until advanced stages when peritoneal dissemination has already occurred. Here, we sought to identify HGSOC-specific alterations in DNA methylation and assess their potential to provide sensitive and specific detection of HGSOC at its earliest stages. EXPERIMENTAL DESIGN MethylationEPIC genome-wide methylation analysis was performed on a discovery cohort comprising 23 HGSOC, 37 non-HGSOC malignant, and 36 histologically unremarkable gynecologic tissue samples. The resulting data were processed using selective bioinformatic criteria to identify regions of high-confidence HGSOC-specific differential methylation. Quantitative methylation-specific real-time PCR (qMSP) assays were then developed for 8 of the top-performing regions and analytically validated in a cohort of 90 tissue samples. Lastly, qMSP assays were used to assess and compare methylation in 30 laser-capture microdissected (LCM) fallopian tube epithelia samples obtained from cancer-free and serous tubal intraepithelial carcinoma (STIC) positive women. RESULTS Bioinformatic selection identified 91 regions of robust, HGSOC-specific hypermethylation, 23 of which exhibited an area under the receiver-operator curve (AUC) value ≥ 0.9 in the discovery cohort. Seven of 8 top-performing regions demonstrated AUC values between 0.838 and 0.968 when analytically validated by qMSP in a 90-patient cohort. A panel of the 3 top-performing genes (c17orf64, IRX2, and TUBB6) was able to perfectly discriminate HGSOC (AUC 1.0). Hypermethylation within these loci was found exclusively in LCM fallopian tube epithelia from women with STIC lesions, but not in cancer-free fallopian tubes. CONCLUSIONS A panel of methylation biomarkers can be used to accurately identify HGSOC, even at precursor stages of the disease.
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Affiliation(s)
- Thomas R Pisanic
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland.
| | - Leslie M Cope
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Oncology and Biostatistics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Shiou-Fu Lin
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ting-Tai Yen
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Pornpat Athamanolap
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ryoichi Asaka
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kentaro Nakayama
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo, Japan
| | - Amanda N Fader
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tza-Huei Wang
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Ie-Ming Shih
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tian-Li Wang
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland. .,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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727
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Hannon E, Knox O, Sugden K, Burrage J, Wong CCY, Belsky DW, Corcoran DL, Arseneault L, Moffitt TE, Caspi A, Mill J. Characterizing genetic and environmental influences on variable DNA methylation using monozygotic and dizygotic twins. PLoS Genet 2018; 14:e1007544. [PMID: 30091980 PMCID: PMC6084815 DOI: 10.1371/journal.pgen.1007544] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/06/2018] [Indexed: 12/21/2022] Open
Abstract
Variation in DNA methylation is being increasingly associated with health and disease outcomes. Although DNA methylation is hypothesized to be a mechanism by which both genetic and non-genetic factors can influence the regulation of gene expression, little is known about the extent to which DNA methylation at specific sites is influenced by heritable as well as environmental factors. We quantified DNA methylation in whole blood at age 18 in a birth cohort of 1,464 individuals comprising 426 monozygotic (MZ) and 306 same-sex dizygotic (DZ) twin pairs. Site-specific levels of DNA methylation were more strongly correlated across the genome between MZ than DZ twins. Structural equation models revealed that although the average contribution of additive genetic influences on DNA methylation across the genome was relatively low, it was notably elevated at the highly variable sites characterized by intermediate levels of DNAm that are most relevant for epigenetic epidemiology. Sites at which variable DNA methylation was most influenced by genetic factors were significantly enriched for DNA methylation quantitative trait loci (mQTL) effects, and overlapped with sites where inter-individual variation correlates across tissues. Finally, we show that DNA methylation at sites robustly associated with environmental exposures such as tobacco smoking and obesity is also influenced by additive genetic effects, highlighting the need to control for genetic background in analyses of exposure-associated DNA methylation differences. Estimates of the contribution of genetic and environmental influences to DNA methylation at all sites profiled in this study are available as a resource for the research community (http://www.epigenomicslab.com/online-data-resources). The study of monozygotic (MZ) and dizygotic (DZ) twins provides an opportunity for exploring the extent to which heritable and environmental factors contribute to phenotypic variation in human populations. We exploit the twin study design to explore the factors influencing epigenetic variation between individuals, focussing on DNA methylation, the best-characterized and most stable epigenetic modification. We find that site-specific levels of DNA methylation are more strongly correlated across the genome between MZ than DZ twins. While the average contribution of additive genetic influences on DNA methylation is relatively low, it is notably elevated at sites that are highly variable and have intermediate levels of DNAm, which are most relevant for epigenetic epidemiology. Sites at which variable DNA methylation is strongly influenced by genetic factors are enriched for DNA methylation quantitative trait loci (mQTL) effects, and overlap with sites where inter-individual variation correlates across tissues. Importantly, we show that DNA methylation at sites robustly associated with environmental exposures such as smoking and obesity is also influenced by genetic effects, highlighting the need to control for genetic background in analyses of exposure-associated DNA methylation differences. Finally, we present a searchable database cataloguing the genetic and environmental contributions to variable DNA methylation across the genome (http://www.epigenomicslab.com/online-data-resources).
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Affiliation(s)
- Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Olivia Knox
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Karen Sugden
- Department of Psychology and Neuroscience, Duke University, Durham, NC, United States of America
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Chloe C. Y. Wong
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London United Kingdom
| | - Daniel W. Belsky
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, United States of America
| | - David L. Corcoran
- Center for Genomic and Computational Biology, Duke University, Durham, NC, United States of America
| | - Louise Arseneault
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London United Kingdom
| | - Terrie E. Moffitt
- Department of Psychology and Neuroscience, Duke University, Durham, NC, United States of America
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London United Kingdom
- Center for Genomic and Computational Biology, Duke University, Durham, NC, United States of America
- Department of Psychiatry and Behavioral Sciences, Duke University Medical School, Durham, NC, United States of America
| | - Avshalom Caspi
- Department of Psychology and Neuroscience, Duke University, Durham, NC, United States of America
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London United Kingdom
- Center for Genomic and Computational Biology, Duke University, Durham, NC, United States of America
- Department of Psychiatry and Behavioral Sciences, Duke University Medical School, Durham, NC, United States of America
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
- * E-mail:
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728
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Cardenas A, Gagné-Ouellet V, Allard C, Brisson D, Perron P, Bouchard L, Hivert MF. Placental DNA Methylation Adaptation to Maternal Glycemic Response in Pregnancy. Diabetes 2018; 67:1673-1683. [PMID: 29752424 DOI: 10.2337/db18-0123] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/04/2018] [Indexed: 11/13/2022]
Abstract
Maternal hyperglycemia during pregnancy is associated with excess fetal growth and adverse perinatal and developmental outcomes. Placental epigenetic maladaptation may underlie these associations. We performed an epigenome-wide association study (>850,000 CpG sites) of term placentas and prenatal maternal glycemic response 2-h post oral glucose challenge at 24-30 weeks of gestation among 448 mother-infant pairs. Maternal 2-h glycemia postload was strongly associated with lower DNA methylation of four CpG sites (false discovery rate [FDR] q <0.05) within the phosphodiesterase 4B gene (PDE4B). Additionally, three other individual CpG sites were differentially methylated relative to maternal glucose response within the TNFRSF1B, LDLR, and BLM genes (FDR q <0.05). DNA methylation correlated with expression of its respective genes in placental tissue at three out of four independent identified loci: PDE4B (r = 0.31, P < 0.01), TNFRSF1B (r = -0.24, P = 0.013), and LDLR (r = 0.32, P < 0.001). In an independent replication cohort (N = 65-108 samples), results were consistent in direction but not significantly replicated among tested CpG sites in PDE4B and TNFRSF1B Our study provides evidence that maternal glycemic response during pregnancy is associated with placental DNA methylation of key inflammatory genes whose expression levels are partially under epigenetic control.
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MESH Headings
- Adult
- Biomarkers/blood
- Biomarkers/metabolism
- Birth Weight
- Cohort Studies
- CpG Islands
- Cyclic Nucleotide Phosphodiesterases, Type 4/genetics
- Cyclic Nucleotide Phosphodiesterases, Type 4/metabolism
- DNA Methylation
- Epigenesis, Genetic
- Female
- Gene Expression Regulation, Developmental
- Glucose Tolerance Test
- Glycated Hemoglobin/analysis
- Humans
- Infant, Newborn
- Insulin Resistance
- Placenta/enzymology
- Placenta/metabolism
- Placentation
- Pregnancy
- Prospective Studies
- RecQ Helicases/genetics
- RecQ Helicases/metabolism
- Receptors, LDL/genetics
- Receptors, LDL/metabolism
- Receptors, Tumor Necrosis Factor, Type II/genetics
- Receptors, Tumor Necrosis Factor, Type II/metabolism
- Term Birth
- Young Adult
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Affiliation(s)
- Andres Cardenas
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA
| | - Valerie Gagné-Ouellet
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Catherine Allard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Diane Brisson
- Lipidology Unit, Community Genomic Medicine Centre and ECOGENE-21, Department of Medicine, Université de Montréal, Saguenay, Quebec, Canada
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Luigi Bouchard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Quebec, Canada
- Diabetes Unit, Massachusetts General Hospital, Boston, MA
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729
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Tan J, Tsakok FHM, Ow EK, Lanskey B, Lim KSD, Goh LG, Tan CH, Cheah IKM, Larbi A, Foo R, Loh M, Wong CKY, Suckling J, Li J, Mahendran R, Kua EH, Feng L. Study Protocol for a Randomized Controlled Trial of Choral Singing Intervention to Prevent Cognitive Decline in At-Risk Older Adults Living in the Community. Front Aging Neurosci 2018; 10:195. [PMID: 30042673 PMCID: PMC6048740 DOI: 10.3389/fnagi.2018.00195] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/11/2018] [Indexed: 12/18/2022] Open
Abstract
Introduction: This study is a parallel-arm randomized controlled trial evaluating choral singing’s efficacy and underlying mechanisms in preventing cognitive decline in at-risk older participants. Methods: Three-hundred and sixty community-dwelling, non-demented older participants are recruited for a 2-year intervention. Inclusion criteria are self-reported cognitive complaints, early cognitive impairment based on neuropsychological test scores or multiple risk factors of dementia. Participants are randomized to either weekly choral singing sessions or general health education. The primary outcome is cognitive performance, measured by a composite cognitive test score (CCTS). Secondary outcomes include depression, anxiety and neuropsychiatric symptoms; perceived stress; sleep quality and severity of dementia symptoms. Underlying mechanisms are examined using blood- and urine-based biomarkers and neuroimaging. Results: Screening began in July 2016. The first group of participants (n = 93) have been recruited. Intervention and control treatments are ongoing and will end in December 2019. Discussion: An evidence-based singing intervention for dementia prevention holds potential for healthcare savings and societal welfare. Trial Registration: NCT02919748, IRB Approval Number: NUS 2508.
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Affiliation(s)
- Jasmine Tan
- Department of Psychology, Goldsmiths, University of London, London, United Kingdom
| | | | - Elisabeth K Ow
- Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Bernard Lanskey
- Yong Siew Toh Conservatory of Music, National University of Singapore, Singapore, Singapore
| | | | - Lee Gan Goh
- Division of Family Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chay-Hoon Tan
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Irwin Kee-Mun Cheah
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Anis Larbi
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Roger Foo
- Genome Institue of Singapore (GIS), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Marie Loh
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | | | - John Suckling
- Department of Psychiatry, University of Cambridge and Cambridge and Peterborough NHS Foundation Trust, Cambridge, United Kingdom
| | - Jialiang Li
- Department of Statistics & Applied Probability, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Rathi Mahendran
- Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ee-Heok Kua
- Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Lei Feng
- Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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730
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Trivedi MS, Oltra E, Sarria L, Rose N, Beljanski V, Fletcher MA, Klimas NG, Nathanson L. Identification of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome-associated DNA methylation patterns. PLoS One 2018; 13:e0201066. [PMID: 30036399 PMCID: PMC6056050 DOI: 10.1371/journal.pone.0201066] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 07/07/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex condition involving multiple organ systems and characterized by persistent/relapsing debilitating fatigue, immune dysfunction, neurological problems, and other symptoms not curable for at least 6 months. Disruption of DNA methylation patterns has been tied to various immune and neurological diseases; however, its status in ME/CFS remains uncertain. Our study aimed at identifying changes in the DNA methylation patterns that associate with ME/CFS. METHODS We extracted genomic DNA from peripheral blood mononuclear cells from 13 ME/CFS study subjects and 12 healthy controls and measured global DNA methylation by ELISA-like method and site-specific methylation status using Illumina MethylationEPIC microarrays. Pyrosequencing validation included 33 ME/CFS cases and 31 controls from two geographically distant cohorts. RESULTS Global DNA methylation levels of ME/CFS cases were similar to those of controls. However, microarray-based approach allowed detection of 17,296 differentially methylated CpG sites in 6,368 genes across regulatory elements and within coding regions of genes. Analysis of DNA methylation in promoter regions revealed 307 differentially methylated promoters. Ingenuity pathway analysis indicated that genes associated with differentially methylated promoters participated in at least 15 different pathways mostly related to cell signaling with a strong immune component. CONCLUSIONS This is the first study that has explored genome-wide epigenetic changes associated with ME/CFS using the advanced Illumina MethylationEPIC microarrays covering about 850,000 CpG sites in two geographically distant cohorts of ME/CFS cases and matched controls. Our results are aligned with previous studies that indicate a dysregulation of the immune system in ME/CFS. They also suggest a potential role of epigenetic de-regulation in the pathobiology of ME/CFS. We propose screening of larger cohorts of ME/CFS cases to determine the external validity of these epigenetic changes in order to implement them as possible diagnostic markers in clinical setting.
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Affiliation(s)
- Malav S. Trivedi
- College of Pharmacy, Nova Southeastern University, Fort Lauderdale, United States of America
| | - Elisa Oltra
- School of Medicine and Dentistry, Catholic University of Valencia, Valencia, Spain
| | - Leonor Sarria
- Institute for Neuro Immune Medicine, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, United States of America
| | - Natasha Rose
- College of Pharmacy, Nova Southeastern University, Fort Lauderdale, United States of America
| | - Vladimir Beljanski
- Cell Therapy Institute, Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, United States of America
| | - Mary Ann Fletcher
- Institute for Neuro Immune Medicine, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, United States of America
- Miami VAMC, Miami, Florida, United States of America
| | - Nancy G. Klimas
- Institute for Neuro Immune Medicine, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, United States of America
- Miami VAMC, Miami, Florida, United States of America
| | - Lubov Nathanson
- Institute for Neuro Immune Medicine, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, United States of America
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731
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Hernandez Mora JR, Tayama C, Sánchez-Delgado M, Monteagudo-Sánchez A, Hata K, Ogata T, Medrano J, Poo-Llanillo ME, Simón C, Moran S, Esteller M, Tenorio J, Lapunzina P, Kagami M, Monk D, Nakabayashi K. Characterization of parent-of-origin methylation using the Illumina Infinium MethylationEPIC array platform. Epigenomics 2018; 10:941-954. [PMID: 29962238 DOI: 10.2217/epi-2017-0172] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
AIM This study aimed to establish a catalog of probes corresponding to imprinted differentially methylated regions (DMRs) on the Infinium HumanMethylationEPIC BeadChip. MATERIALS & METHODS Reciprocal uniparental diploidies with low normal biparental mosaic contribution, together with normal diploid controls, were subjected to EPIC BeadChip hybridization. The methylation profiles were assessed for imprinted differential methylation. Top candidates were validated using locus-specific PCR-based assays. RESULTS Seven hundred and eighty-nine CpG probes coincided with 50 known imprinted DMRs and 467 CpG probes corresponding to 124 novel imprinted DMR candidates were identified. Validation led to identification of several subtle DMRs within known imprinted domains as well as novel maternally methylated regions associated with PTCHD3 and JAKMIP1. CONCLUSION Our comprehensive list of bona fide-imprinted DMR probes will simplify and facilitate methylation profiling of individuals with imprinting disorders and is applicable to other diseases in which aberrant imprinting has been implicated, such as cancer and fetal growth.
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Affiliation(s)
- Jose R Hernandez Mora
- Imprinting & Cancer group, Cancer Epigenetic & Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health & Development, Tokyo, Japan
| | - Marta Sánchez-Delgado
- Imprinting & Cancer group, Cancer Epigenetic & Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ana Monteagudo-Sánchez
- Imprinting & Cancer group, Cancer Epigenetic & Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health & Development, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Jose Medrano
- Fundación IVI-Instituto Universitario IVI- INCLIVA, Valencia, Spain
| | | | - Carlos Simón
- Igenomix SL, Valencia, Spain.,Department of Obs/Gyn, Valencia University, Valencia, Spain.,Department of Obs/Gyn, Stanford University, Palo Alto, CA 94305, USA
| | - Sebastian Moran
- Cancer Epigenetics group, Cancer Epigenetic & Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics group, Cancer Epigenetic & Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Jair Tenorio
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health & Development, Tokyo, Japan
| | - David Monk
- Imprinting & Cancer group, Cancer Epigenetic & Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health & Development, Tokyo, Japan
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732
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Philibert R, Dogan M, Noel A, Miller S, Krukow B, Papworth E, Cowley J, Knudsen A, Beach SR, Black D. Genome-wide and digital polymerase chain reaction epigenetic assessments of alcohol consumption. Am J Med Genet B Neuropsychiatr Genet 2018; 177:479-488. [PMID: 29704316 PMCID: PMC9518929 DOI: 10.1002/ajmg.b.32636] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/13/2018] [Accepted: 03/27/2018] [Indexed: 01/19/2023]
Abstract
The lack of readily employable biomarkers of alcohol consumption is a problem for clinicians and researchers. In 2014, we published a preliminary DNA methylation signature of heavy alcohol consumption that remits as a function of abstinence. Herein, we present new genome-wide methylation findings from a cohort of additional subjects and a meta-analysis of the data. Using DNA from 47 consecutive heavy drinkers admitted for alcohol detoxification in the context of alcohol treatment and 47 abstinent controls, we replicate the 2014 results and show that 21,221 CpG residues are differentially methylated in active heavy drinkers. Meta-analysis of all data from the 448,058 probes common to the two methylation platforms shows a similarly profound signature with confirmation of findings from other groups. Principal components analyses show that genome-wide methylation changes in response to alcohol consumption load on two major factors with one component accounting at least 50% of the total variance in both smokers and nonsmoking alcoholics. Using data from the arrays, we derive a panel of five methylation probes that classifies use status with a receiver operator characteristic area under the curve (AUC) of 0.97. Finally, using droplet digital polymerase chain reaction (PCR), we convert these array-based findings to two marker assays with an AUC of 0.95 and a four marker set AUC of 0.98. We conclude that DNA methylation assessments are capable of quantifying alcohol use status and suggest that readily employable digital PCR approaches for substance consumption may find widespread use in alcohol-related research and patient care.
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Affiliation(s)
- Robert Philibert
- Behavioral Diagnostics, Coralville, Iowa 52241,Department of Psychiatry, University of Iowa, Iowa City, IA 52242,to whom correspondence should be addressed at: 2500 Crosspark Road, Suite W245, Coralville, IA 52241,
| | - Meesha Dogan
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242,Cardio Diagnostics, Coralville, Iowa 52241
| | - Amanda Noel
- Behavioral Diagnostics, Coralville, Iowa 52241
| | | | | | | | - Joseph Cowley
- Center for Alcohol and Drug Services, Davenport, IA 52804
| | | | | | - Donald Black
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242
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733
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Tejedor JR, Bueno C, Cobo I, Bayón GF, Prieto C, Mangas C, Pérez RF, Santamarina P, Urdinguio RG, Menéndez P, Fraga MF, Fernández AF. Epigenome-wide analysis reveals specific DNA hypermethylation of T cells during human hematopoietic differentiation. Epigenomics 2018; 10:903-923. [DOI: 10.2217/epi-2017-0163] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Aim: Epigenetic regulation plays an important role in cellular development and differentiation. A detailed map of the DNA methylation dynamics that occur during cell differentiation would contribute to decipher the molecular networks governing cell fate commitment. Methods: Illumina MethylationEPIC BeadChip platform was used to describe the genome-wide DNA methylation changes observed throughout hematopoietic maturation by analyzing multiple myeloid and lymphoid hematopoietic cell types. Results: We identified a plethora of DNA methylation changes that occur during human hematopoietic differentiation. We observed that T lymphocytes display substantial enhancement of de novo CpG hypermethylation as compared with other hematopoietic cell populations. T-cell-specific hypermethylated regions were strongly associated with open chromatin marks and enhancer elements, as well as binding sites of specific key transcription factors involved in hematopoietic differentiation, such as PU.1 and TAL1. Conclusion: These results provide novel insights into the role of DNA methylation at enhancer elements in T-cell development.
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Affiliation(s)
- J Ramón Tejedor
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Principado de Asturias, Spain
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Principado de Asturias, Spain
| | - Clara Bueno
- Department of Biomedicine, School of Medicine, Josep Carreras Leukemia Research Institute, University of Barcelona, Barcelona, Spain
| | - Isabel Cobo
- Department of Biomedicine, School of Medicine, Josep Carreras Leukemia Research Institute, University of Barcelona, Barcelona, Spain
| | - Gustavo F Bayón
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Principado de Asturias, Spain
| | - Cristina Prieto
- Department of Biomedicine, School of Medicine, Josep Carreras Leukemia Research Institute, University of Barcelona, Barcelona, Spain
| | - Cristina Mangas
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Principado de Asturias, Spain
| | - Raúl F Pérez
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Principado de Asturias, Spain
- Nanomaterials & Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Spain
| | - Pablo Santamarina
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Principado de Asturias, Spain
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Principado de Asturias, Spain
| | - Rocío G Urdinguio
- Nanomaterials & Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Spain
| | - Pablo Menéndez
- Department of Biomedicine, School of Medicine, Josep Carreras Leukemia Research Institute, University of Barcelona, Barcelona, Spain
- Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Josep Carreras Leukemia Research Institute-Campus ICO, Research Institut Germans Trias i Pujol (IGTP), Badalona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), ISCIII, Barcelona, Spain
| | - Mario F Fraga
- Nanomaterials & Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Principado de Asturias, Spain
| | - Agustín F Fernández
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Principado de Asturias, Spain
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Principado de Asturias, Spain
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734
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De Witte SF, Peters FS, Merino A, Korevaar SS, Van Meurs JB, O'Flynn L, Elliman SJ, Newsome PN, Boer K, Baan CC, Hoogduijn MJ. Epigenetic changes in umbilical cord mesenchymal stromal cells upon stimulation and culture expansion. Cytotherapy 2018; 20:919-929. [DOI: 10.1016/j.jcyt.2018.05.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/26/2018] [Accepted: 05/08/2018] [Indexed: 12/18/2022]
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735
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Nieto T, Tomlinson CL, Dretzke J, Bayliss S, Price MJ, Dilworth M, Beggs AD, Tucker O. A systematic review of epigenetic biomarkers in progression from non-dysplastic Barrett's oesophagus to oesophageal adenocarcinoma. BMJ Open 2018; 8:e020427. [PMID: 29961009 PMCID: PMC6042533 DOI: 10.1136/bmjopen-2017-020427] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 04/16/2018] [Accepted: 05/03/2018] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES The objective of this systematic review is to identify and summarise studies which examine epigenetic biomarkers in patients with Barrett's oesophagus (BO) and their association with progression to oesophageal adenocarcinoma (OADC). BO is a precursor lesion for OADC. There is no clinical test to predict patients who are likely to progress to OADC. An epigenetic biomarker could predict patients who are at high risk of progression from BO to OADC which could facilitate earlier diagnosis and spare those unlikely to develop cancer from regular invasive surveillance endoscopy. SETTING A systematic search was conducted of the following databases: MEDLINE, MEDLINE in Process, EMBASE, Cochrane Central, ISI Conference Proceedings Citation Index and the British Library's ZETOC. Studies were conducted in secondary and tertiary care settings. PARTICIPANTS All studies measuring epigenetic change in patients over 18 years old who progressed from non-dysplastic BO to OADC were included. Genetic, in vitro and studies which did not measure progression in the same patient cohort were excluded. Study inclusion and risk of bias of individual eligible studies were assessed in duplicate by two reviewers using a modified Quality in Prognostic Studies tool. RESULTS 14 studies met the inclusion criteria. 42 epigenetic markers were identified, and 5 studies developed models aiming to predict progression to OADC. CONCLUSIONS The evidence from this systematic review is suggestive of a role for p16 as an epigenetic biomarker for the progression of BO to OADC. PROSPERO NUMBER CRD42016038654.
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Affiliation(s)
- Tom Nieto
- Department of Surgery, University of Birmingham, Birmingham, UK
| | - Claire L Tomlinson
- Birmingham Clinical Trials Unit, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Janine Dretzke
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Susan Bayliss
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Malcolm James Price
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Mark Dilworth
- Department of Surgery, Heart of England Foundation Trust and Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Andrew D Beggs
- Department of Surgery, University of Birmingham, Birmingham, UK
| | - Olga Tucker
- Department of Surgery, University of Birmingham, Birmingham, UK
- Department of Surgery, Heart of England Foundation Trust and Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
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736
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Nair SS, Luu PL, Qu W, Maddugoda M, Huschtscha L, Reddel R, Chenevix-Trench G, Toso M, Kench JG, Horvath LG, Hayes VM, Stricker PD, Hughes TP, White DL, Rasko JEJ, Wong JJL, Clark SJ. Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten. Epigenetics Chromatin 2018; 11:24. [PMID: 29807544 PMCID: PMC5971424 DOI: 10.1186/s13072-018-0194-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/21/2018] [Indexed: 12/24/2022] Open
Abstract
Background Comprehensive genome-wide DNA methylation profiling is critical to gain insights into epigenetic reprogramming during development and disease processes. Among the different genome-wide DNA methylation technologies, whole genome bisulphite sequencing (WGBS) is considered the gold standard for assaying genome-wide DNA methylation at single base resolution. However, the high sequencing cost to achieve the optimal depth of coverage limits its application in both basic and clinical research. To achieve 15× coverage of the human methylome, using WGBS, requires approximately three lanes of 100-bp-paired-end Illumina HiSeq 2500 sequencing. It is important, therefore, for advances in sequencing technologies to be developed to enable cost-effective high-coverage sequencing. Results In this study, we provide an optimised WGBS methodology, from library preparation to sequencing and data processing, to enable 16–20× genome-wide coverage per single lane of HiSeq X Ten, HCS 3.3.76. To process and analyse the data, we developed a WGBS pipeline (METH10X) that is fast and can call SNPs. We performed WGBS on both high-quality intact DNA and degraded DNA from formalin-fixed paraffin-embedded tissue. First, we compared different library preparation methods on the HiSeq 2500 platform to identify the best method for sequencing on the HiSeq X Ten. Second, we optimised the PhiX and genome spike-ins to achieve higher quality and coverage of WGBS data on the HiSeq X Ten. Third, we performed integrated whole genome sequencing (WGS) and WGBS of the same DNA sample in a single lane of HiSeq X Ten to improve data output. Finally, we compared methylation data from the HiSeq 2500 and HiSeq X Ten and found high concordance (Pearson r > 0.9×). Conclusions Together we provide a systematic, efficient and complete approach to perform and analyse WGBS on the HiSeq X Ten. Our protocol allows for large-scale WGBS studies at reasonable processing time and cost on the HiSeq X Ten platform. Electronic supplementary material The online version of this article (10.1186/s13072-018-0194-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shalima S Nair
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Phuc-Loi Luu
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Wenjia Qu
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Madhavi Maddugoda
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Lily Huschtscha
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Roger Reddel
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | | | | | - James G Kench
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Lisa G Horvath
- Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia.,Clinical Prostate Cancer Research, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Chris O'Brien Lifehouse, Camperdown, NSW, Australia
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Phillip D Stricker
- Department of Urology, St. Vincent's Hospital, Darlinghurst, NSW, Australia
| | - Timothy P Hughes
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,Australian Leukaemia and Lymphoma Group, Melbourne, Australia.,Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia.,Department of Haematology, SA Pathology, Adelaide, SA, Australia
| | - Deborah L White
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,Australian Leukaemia and Lymphoma Group, Melbourne, Australia.,Faculty of Health Science and Faculty of Science, University of Adelaide, Adelaide, SA, Australia.,Australian Genomic Health Alliance, Melbourne, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, Australia
| | - Justin J-L Wong
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Susan J Clark
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia. .,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia. .,Epigenetics Research Program, The Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW, 2010, Australia.
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737
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Kacmarczyk TJ, Fall MP, Zhang X, Xin Y, Li Y, Alonso A, Betel D. "Same difference": comprehensive evaluation of four DNA methylation measurement platforms. Epigenetics Chromatin 2018; 11:21. [PMID: 29801521 PMCID: PMC5970534 DOI: 10.1186/s13072-018-0190-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/21/2018] [Indexed: 12/17/2022] Open
Abstract
Background DNA methylation in CpG context is fundamental to the epigenetic regulation of gene expression in higher eukaryotes. Changes in methylation patterns are implicated in many diseases, cellular differentiation, imprinting, and other biological processes. Techniques that enrich for biologically relevant genomic regions with high CpG content are desired, since, depending on the size of an organism’s methylome, the depth of sequencing required to cover all CpGs can be prohibitively expensive. Currently, restriction enzyme-based reduced representation bisulfite sequencing and its modified protocols are widely used to study methylation differences. Recently, Agilent Technologies, Roche NimbleGen, and Illumina have ventured to both reduce sequencing costs and capture CpGs of known biological relevance by marketing in-solution custom-capture hybridization platforms. We aimed to evaluate the similarities and differences of these four methods considering each platform targets approximately 10–13% of the human methylome. Results Overall, the regions covered per platform were as expected: targeted capture-based methods covered > 95% of their designed regions, whereas the restriction enzyme-based method covered > 70% of the expected fragments. While the total number of CpG loci shared by all methods was low, ~ 24% of any platform, the methylation levels of CpGs covered by all platforms were concordant. Annotation of CpG loci with genomic features revealed roughly the same proportions of feature annotations across the four platforms. Targeted capture methods comprise similar types and coverage of annotations and, relative to the targeted methods, the restriction enzyme method covers fewer promoters (~ 9%), CpG shores (~ 8%) and unannotated loci (~ 11%). Conclusions Although all methods are largely consistent in terms of covered CpG loci, the commercially available capture methods result in covering nearly all CpG sites in their target regions with few off-target loci and covering similar proportions of annotated CpG loci, the restriction-based enrichment results in more off-target and unannotated CpG loci. Quality of DNA is very important for restriction-based enrichment and starting material can be low. Conversely, quality of the starting material is less important for capture methods, and at least twice the amount of starting material is required. Pricing is marginally less for restriction-based enrichment, and the number of samples that can be prepared is not restricted to the number of capture reactions a kit supports. However, the advantage of capture libraries is the ability to custom design areas of interest. The choice of the technique would be decided by the number of samples, the quality and quantity of DNA available and the biological areas of interest since comparable data are obtained from all platforms. Electronic supplementary material The online version of this article (10.1186/s13072-018-0190-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thadeous J Kacmarczyk
- Division of Hematology/Oncology, Department of Medicine, Epigenomics Core Facility, Weill Cornell Medicine, New York, NY, USA.
| | - Mame P Fall
- Division of Hematology/Oncology, Department of Medicine, Epigenomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Xihui Zhang
- Division of Hematology/Oncology, Department of Medicine, Epigenomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Yuan Xin
- Division of Hematology/Oncology, Department of Medicine, Epigenomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Yushan Li
- Division of Hematology/Oncology, Department of Medicine, Epigenomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Alicia Alonso
- Division of Hematology/Oncology, Department of Medicine, Epigenomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Doron Betel
- Division of Hematology/Oncology, Department of Medicine, Epigenomics Core Facility, Weill Cornell Medicine, New York, NY, USA.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
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738
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Zou LS, Erdos MR, Taylor DL, Chines PS, Varshney A, Parker SCJ, Collins FS, Didion JP. BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues. BMC Genomics 2018; 19:390. [PMID: 29792182 PMCID: PMC5966887 DOI: 10.1186/s12864-018-4766-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/08/2018] [Indexed: 01/14/2023] Open
Abstract
Background Bisulfite sequencing is widely employed to study the role of DNA methylation in disease; however, the data suffer from biases due to coverage depth variability. Imputation of methylation values at low-coverage sites may mitigate these biases while also identifying important genomic features associated with predictive power. Results Here we describe BoostMe, a method for imputing low-quality DNA methylation estimates within whole-genome bisulfite sequencing (WGBS) data. BoostMe uses a gradient boosting algorithm, XGBoost, and leverages information from multiple samples for prediction. We find that BoostMe outperforms existing algorithms in speed and accuracy when applied to WGBS of human tissues. Furthermore, we show that imputation improves concordance between WGBS and the MethylationEPIC array at low WGBS depth, suggesting improved WGBS accuracy after imputation. Conclusions Our findings support the use of BoostMe as a preprocessing step for WGBS analysis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4766-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luli S Zou
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael R Erdos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - D Leland Taylor
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Peter S Chines
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Arushi Varshney
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Stephen C J Parker
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Francis S Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - John P Didion
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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739
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Lapato DM, Moyer S, Olivares E, Amstadter AB, Kinser PA, Latendresse SJ, Jackson-Cook C, Roberson-Nay R, Strauss JF, York TP. Prospective longitudinal study of the pregnancy DNA methylome: the US Pregnancy, Race, Environment, Genes (PREG) study. BMJ Open 2018; 8:e019721. [PMID: 29743320 PMCID: PMC5942473 DOI: 10.1136/bmjopen-2017-019721] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 01/15/2018] [Accepted: 02/16/2018] [Indexed: 01/08/2023] Open
Abstract
PURPOSE The goal of the Pregnancy, Race, Environment, Genes study was to understand how social and environmental determinants of health (SEDH), pregnancy-specific environments (PSE) and biological processes influence the timing of birth and account for the racial disparity in preterm birth. The study followed a racially diverse longitudinal cohort throughout pregnancy and included repeated measures of PSE and DNA methylation (DNAm) over the course of gestation and up to 1 year into the postpartum period. PARTICIPANTS All women were between 18 and 40 years of age with singleton pregnancies and no diagnosis of diabetes or indication of assisted reproductive technology. Both mother and father had to self-identify as either African-American (AA) or European-American (EA). Maternal peripheral blood samples along with self-report questionnaires measuring SEDH and PSE factors were collected at four pregnancy visits, and umbilical cord blood was obtained at birth. A subset of participants returned for two additional postpartum visits, during which additional questionnaires and maternal blood samples were collected. The pregnancy and postpartum extension included n=240 (AA=126; EA=114) and n=104 (AA=50; EA=54), respectively. FINDINGS TO DATE One hundred seventy-seven women (AA=89, EA=88) met full inclusion criteria out of a total of 240 who were initially enrolled. Of the 63 participants who met exclusion criteria after enrolment, 44 (69.8%) were associated with a medical reason. Mean gestational age at birth was significantly shorter for the AA participants by 5.1 days (M=272.5 (SD=10.5) days vs M=277.6 (SD=8.3)). FUTURE PLANS Future studies will focus on identifying key environmental factors that influence DNAm change across pregnancy and account for racial differences in preterm birth.
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Affiliation(s)
- Dana M Lapato
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Sara Moyer
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, Virginia, USA
| | | | - Ananda B Amstadter
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Patricia A Kinser
- Department of Family and Community Health Nursing, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Shawn J Latendresse
- Department of Psychology and Neuroscience, Baylor University, Waco, Texas, USA
| | - Colleen Jackson-Cook
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Roxann Roberson-Nay
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Jerome F Strauss
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Timothy P York
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, Virginia, USA
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740
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Troisi R, Bjørge T, Gissler M, Grotmol T, Kitahara CM, Sæther SMM, Ording AG, Sköld C, Sørensen HT, Trabert B, Glimelius I. The role of pregnancy, perinatal factors and hormones in maternal cancer risk: a review of the evidence. J Intern Med 2018; 283:430-445. [PMID: 29476569 PMCID: PMC6688839 DOI: 10.1111/joim.12747] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An understanding of the origin of cancer is critical for cancer prevention and treatment. Complex biological mechanisms promote carcinogenesis, and there is increasing evidence that pregnancy-related exposures influence foetal growth cell division and organ functioning and may have a long-lasting impact on health and disease susceptibility in the mothers and offspring. Nulliparity is an established risk factor for breast, ovarian, endometrial and possibly pancreatic cancer, whilst the risk of kidney cancer is elevated in parous compared with nulliparous women. For breast, endometrial and ovarian cancer, each pregnancy provides an additional risk reduction. The associations of parity with thyroid and colorectal cancers are uncertain. The timing of reproductive events is also recognized to be important. Older age at first birth is associated with an increased risk of breast cancer, and older age at last birth is associated with a reduced risk of endometrial cancer. The risks of breast and endometrial cancers increase with younger age at menarche and older age at menopause. The mechanisms, and hormone profiles, that underlie alterations in maternal cancer risk are not fully understood and may differ by malignancy. Linking health registries and pooling of data in the Nordic countries have provided opportunities to conduct epidemiologic research of pregnancy exposures and subsequent cancer. We review the maternal risk of several malignancies, including those with a well-known hormonal aetiology and those with less established relationships. The tendency for women to have fewer pregnancies and at later ages, together with the age-dependent increase in the incidence of most malignancies, is expected to affect the incidence of pregnancy-associated cancer.
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Affiliation(s)
- Rebecca Troisi
- Division of Cancer Epidemiology and Biostatistics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Tone Bjørge
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Cancer Registry of Norway, Oslo, Norway
| | - Mika Gissler
- Information Services Department, National Institute for Health and Welfare (THL), Helsinki, Finland
- Department of Neurobiology, Care Sciences and Society, Division of Family Medicine, Karolinska Institute, Stockholm, Sweden
| | | | - Cari M. Kitahara
- Division of Cancer Epidemiology and Biostatistics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | | | - Anne Gulbech Ording
- Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark
| | - Camilla Sköld
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Henrik Toft Sørensen
- Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark
| | - Britton Trabert
- Division of Cancer Epidemiology and Biostatistics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Ingrid Glimelius
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Department of Medicine, Clinical Epidemiology Unit, Karolinska Institutet Stockholm, Sweden
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741
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Jiao C, Zhang C, Dai R, Xia Y, Wang K, Giase G, Chen C, Liu C. Positional effects revealed in Illumina methylation array and the impact on analysis. Epigenomics 2018; 10:643-659. [PMID: 29469594 PMCID: PMC6021926 DOI: 10.2217/epi-2017-0105] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 01/17/2018] [Indexed: 12/18/2022] Open
Abstract
AIM We aimed to prove the existence of positional effects in the Illumina methylation beadchip data and to find an optimal correction method. MATERIALS & METHODS Three HumanMethylation450, three HumanMethylation27 datasets and two EPIC datasets were analyzed. ComBat, linear regression, functional normalization and single-sample Noob were used for minimizing positional effects. The corrected results were evaluated by four methods. RESULTS We detected 52,988 CpG loci significantly associated with sample positions, 112 remained after ComBat correction in the primary dataset. The pre- and postcorrection comparisons indicate the positional effects could alter the measured methylation values and downstream analysis results. CONCLUSION Positional effects exist in the Illumina methylation array and may bias the analyses. Using ComBat to correct positional effects is recommended.
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Affiliation(s)
- Chuan Jiao
- Center for Medical Genetics, Central South University, Changsha, Hunan 410012, PR China
| | - Chunling Zhang
- Department of Neurology and Physiology, SUNY Upstate Medical University, Syracuse, NY 13201, USA
| | - Rujia Dai
- Center for Medical Genetics, Central South University, Changsha, Hunan 410012, PR China
| | - Yan Xia
- Center for Medical Genetics, Central South University, Changsha, Hunan 410012, PR China
| | - Kangli Wang
- Center for Medical Genetics, Central South University, Changsha, Hunan 410012, PR China
| | - Gina Giase
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Chao Chen
- Center for Medical Genetics, Central South University, Changsha, Hunan 410012, PR China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, Hunan 410012, PR China
| | - Chunyu Liu
- Center for Medical Genetics, Central South University, Changsha, Hunan 410012, PR China
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13201, USA
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742
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Philibert R, Dogan M, Noel A, Miller S, Krukow B, Papworth E, Cowley J, Long JD, Beach SRH, Black DW. Dose Response and Prediction Characteristics of a Methylation Sensitive Digital PCR Assay for Cigarette Consumption in Adults. Front Genet 2018; 9:137. [PMID: 29740475 PMCID: PMC5928210 DOI: 10.3389/fgene.2018.00137] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/03/2018] [Indexed: 01/16/2023] Open
Abstract
The tobacco use disorders are the largest preventable cause of morbidity and mortality in the world. A substantial barrier to the development of better intervention and screening measures is the lack of clinically employable biomarkers to detect the existence and extent of tobacco consumption. In prior work, we and others have shown that array based assessment of DNA methylation status at cg05575921 is a sensitive and quantitative method for assessing cigarette consumption. Unfortunately, in general, arrays are not practical clinical tools. Herein, we detail the prediction performance metrics and dose dependency of a clinically implementable droplet digital PCR (ddPCR) assay for cigarette consumption in adults. First, we demonstrate that measurements of cg05575921 as determined by Illumina array and ddPCR are highly correlated (R2 = 0.98, n = 92). Second, using clinical data and biomaterial from 177 subjects ranging from 18 to 78 years of age, we show that the Receiver Operating Characteristic (ROC) area under the curve (AUC) for classifying smoking status using methylation status at cg05575921 is 0.99. Finally, we conduct modeling analyses of cigarette consumption over discrete time periods to show that methylation status is best correlated with mean cigarette consumption over the past year (R2 = 0.5) and that demethylation at cg05575921 is dose dependent with a demethylation (delta beta) of 1% being equivalent to 1.2 cigarettes per day. But we do not find a relationship between Fagerstrom score and DNA methylation. We conclude that ddPCR assessment of cg05575921 methylation is an accurate method for assessing the presence and extent of cigarette consumption in adult subjects. We suggest that skillful clinical implementation of this approach alone or in combination with other assessment methods could lead to substantial reduction of cigarette consumption related morbidity and mortality.
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Affiliation(s)
- Robert Philibert
- Behavioral Diagnostics LLC, Coralville, IA, United States
- Department of Psychiatry, University of Iowa, Iowa City, IA, United States
| | - Meesha Dogan
- Department of Psychiatry, University of Iowa, Iowa City, IA, United States
- Cardio Diagnostics, Coralville, IA, United States
| | - Amanda Noel
- Behavioral Diagnostics LLC, Coralville, IA, United States
| | - Shelly Miller
- Behavioral Diagnostics LLC, Coralville, IA, United States
| | - Brianna Krukow
- Behavioral Diagnostics LLC, Coralville, IA, United States
| | - Emma Papworth
- Behavioral Diagnostics LLC, Coralville, IA, United States
| | - Joseph Cowley
- Center for Alcohol and Drug Services, Davenport, IA, United States
| | | | - Steven R. H. Beach
- Center for Family Studies at the University of Georgia, Athens, GA, United States
| | - Donald W. Black
- Department of Psychiatry, University of Iowa, Iowa City, IA, United States
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743
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Gallardo-Gómez M, Moran S, Páez de la Cadena M, Martínez-Zorzano VS, Rodríguez-Berrocal FJ, Rodríguez-Girondo M, Esteller M, Cubiella J, Bujanda L, Castells A, Balaguer F, Jover R, De Chiara L. A new approach to epigenome-wide discovery of non-invasive methylation biomarkers for colorectal cancer screening in circulating cell-free DNA using pooled samples. Clin Epigenetics 2018; 10:53. [PMID: 29686738 PMCID: PMC5902929 DOI: 10.1186/s13148-018-0487-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/02/2018] [Indexed: 12/16/2022] Open
Abstract
Background Colorectal cancer is the fourth cause of cancer-related deaths worldwide, though detection at early stages associates with good prognosis. Thus, there is a clear demand for novel non-invasive tests for the early detection of colorectal cancer and premalignant advanced adenomas, to be used in population-wide screening programs. Aberrant DNA methylation detected in liquid biopsies, such as serum circulating cell-free DNA (cfDNA), is a promising source of non-invasive biomarkers. This study aimed to assess the feasibility of using cfDNA pooled samples to identify potential serum methylation biomarkers for the detection of advanced colorectal neoplasia (colorectal cancer or advanced adenomas) using microarray-based technology. Results cfDNA was extracted from serum samples from 20 individuals with no colorectal findings, 20 patients with advanced adenomas, and 20 patients with colorectal cancer (stages I and II). Two pooled samples were prepared for each pathological group using equal amounts of cfDNA from 10 individuals, sex-, age-, and recruitment hospital-matched. We measured the methylation levels of 866,836 CpG positions across the genome using the MethylationEPIC array. Pooled serum cfDNA methylation data meets the quality requirements. The proportion of detected CpG in all pools (> 99% with detection p value < 0.01) exceeded Illumina Infinium methylation data quality metrics of the number of sites detected. The differential methylation analysis revealed 1384 CpG sites (5% false discovery rate) with at least 10% difference in the methylation level between no colorectal findings controls and advanced neoplasia, the majority of which were hypomethylated. Unsupervised clustering showed that cfDNA methylation patterns can distinguish advanced neoplasia from healthy controls, as well as separate tumor tissue from healthy mucosa in an independent dataset. We also observed that advanced adenomas and stage I/II colorectal cancer methylation profiles, grouped as advanced neoplasia, are largely homogenous and clustered close together. Conclusions This preliminary study shows the viability of microarray-based methylation biomarker discovery using pooled serum cfDNA samples as an alternative approach to tissue specimens. Our strategy sets an open door for deciphering new non-invasive biomarkers not only for colorectal cancer detection, but also for other types of cancers.
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Affiliation(s)
- María Gallardo-Gómez
- 1Department of Biochemistry, Genetics and Immunology, Centro Singular de Investigación de Galicia (CINBIO), University of Vigo, Campus As Lagoas-Marcosende s/n, 36310 Vigo, Spain
| | - Sebastian Moran
- 2Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - María Páez de la Cadena
- 1Department of Biochemistry, Genetics and Immunology, Centro Singular de Investigación de Galicia (CINBIO), University of Vigo, Campus As Lagoas-Marcosende s/n, 36310 Vigo, Spain
| | - Vicenta Soledad Martínez-Zorzano
- 1Department of Biochemistry, Genetics and Immunology, Centro Singular de Investigación de Galicia (CINBIO), University of Vigo, Campus As Lagoas-Marcosende s/n, 36310 Vigo, Spain
| | - Francisco Javier Rodríguez-Berrocal
- 1Department of Biochemistry, Genetics and Immunology, Centro Singular de Investigación de Galicia (CINBIO), University of Vigo, Campus As Lagoas-Marcosende s/n, 36310 Vigo, Spain
| | - Mar Rodríguez-Girondo
- 3Department of Medical Statistics and Bioinformatics, Leiden University Medical Centre, Leiden, The Netherlands.,4SiDOR Research Group and Centro de Investigaciones Biomédicas (CINBIO), Faculty of Economics and Business Administration, University of Vigo, Vigo, Spain
| | - Manel Esteller
- 2Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Joaquín Cubiella
- 5Department of Gastroenterology, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Biomédica Galicia Sur, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Ourense, Spain
| | - Luis Bujanda
- 6Department of Gastroenterology, Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
| | - Antoni Castells
- 7Gastroenterology Department, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Francesc Balaguer
- 7Gastroenterology Department, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Rodrigo Jover
- 8Department of Gastroenterology, Hospital General Universitario de Alicante, Alicante, Spain
| | - Loretta De Chiara
- 1Department of Biochemistry, Genetics and Immunology, Centro Singular de Investigación de Galicia (CINBIO), University of Vigo, Campus As Lagoas-Marcosende s/n, 36310 Vigo, Spain
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744
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Wiik A, Andersson DP, Brismar TB, Chanpen S, Dhejne C, Ekström TJ, Flanagan JN, Holmberg M, Kere J, Lilja M, Lindholm ME, Lundberg TR, Maret E, Melin M, Olsson SM, Rullman E, Wåhlén K, Arver S, Gustafsson T. Metabolic and functional changes in transgender individuals following cross-sex hormone treatment: Design and methods of the GEnder Dysphoria Treatment in Sweden (GETS) study. Contemp Clin Trials Commun 2018; 10:148-153. [PMID: 30023449 PMCID: PMC6046513 DOI: 10.1016/j.conctc.2018.04.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 04/05/2018] [Accepted: 04/11/2018] [Indexed: 11/16/2022] Open
Abstract
Background Although the divergent male and female differentiation depends on key genes, many biological differences seen in men and women are driven by relative differences in estrogen and testosterone levels. Gender dysphoria denotes the distress that gender incongruence with the assigned sex at birth may cause. Gender-affirming treatment includes medical intervention such as inhibition of endogenous sex hormones and subsequent replacement with cross-sex hormones. The aim of this study is to investigate consequences of an altered sex hormone profile on different tissues and metabolic risk factors. By studying subjects undergoing gender-affirming medical intervention with sex hormones, we have the unique opportunity to distinguish between genetic and hormonal effects. Methods The study is a single center observational cohort study conducted in Stockholm, Sweden. The subjects are examined at four time points; before initiation of treatment, after endogenous sex hormone inhibition, and three and eleven months following sex hormone treatment. Examinations include blood samples, skeletal muscle-, adipose- and skin tissue biopsies, arteriography, echocardiography, carotid Doppler examination, whole body MRI, CT of muscle and measurements of muscle strength. Results The primary outcome measure is transcriptomic and epigenomic changes in skeletal muscle. Secondary outcome measures include transcriptomic and epigenomic changes associated with metabolism in adipose and skin, muscle strength, fat cell size and ability to release fatty acids from adipose tissue, cardiovascular function, and body composition. Conclusions This study will provide novel information on the role of sex hormone treatment in skeletal muscle, adipose and skin, and its relation to cardiovascular and metabolic disease.
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Affiliation(s)
- Anna Wiik
- Department of Laboratory Medicine, Karolinska Institutet, Unit of Clinical Physiology, Karolinska University Hospital, Stockholm, Sweden
| | - Daniel P. Andersson
- Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Corresponding author. Department of Medicine (H7) C2:94, Karolinska Institutet, 14186 Stockholm, Sweden.
| | - Torkel B. Brismar
- Division of Radiology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Setareh Chanpen
- ANOVA, Andrology, Sexual Medicine and Transgender Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Cecilia Dhejne
- Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
- ANOVA, Andrology, Sexual Medicine and Transgender Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Tomas J. Ekström
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - John N. Flanagan
- Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Mats Holmberg
- ANOVA, Andrology, Sexual Medicine and Transgender Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Mats Lilja
- Department of Laboratory Medicine, Karolinska Institutet, Unit of Clinical Physiology, Karolinska University Hospital, Stockholm, Sweden
| | - Malene E. Lindholm
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Tommy R. Lundberg
- Department of Laboratory Medicine, Karolinska Institutet, Unit of Clinical Physiology, Karolinska University Hospital, Stockholm, Sweden
| | - Eva Maret
- Department of Laboratory Medicine, Karolinska Institutet, Unit of Clinical Physiology, Karolinska University Hospital, Stockholm, Sweden
| | - Michael Melin
- Heart and Vascular Theme, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Sofie M. Olsson
- Department of Laboratory Medicine, Karolinska Institutet, Unit of Clinical Physiology, Karolinska University Hospital, Stockholm, Sweden
| | - Eric Rullman
- Department of Laboratory Medicine, Karolinska Institutet, Unit of Clinical Physiology, Karolinska University Hospital, Stockholm, Sweden
- Heart and Vascular Theme, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Kerstin Wåhlén
- Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Stefan Arver
- Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Thomas Gustafsson
- Department of Laboratory Medicine, Karolinska Institutet, Unit of Clinical Physiology, Karolinska University Hospital, Stockholm, Sweden
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745
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Wang Z, Wu X, Wang Y. A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip. BMC Bioinformatics 2018; 19:115. [PMID: 29671397 PMCID: PMC5907140 DOI: 10.1186/s12859-018-2096-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background DNA methylation has been identified to be widely associated to complex diseases. Among biological platforms to profile DNA methylation in human, the Illumina Infinium HumanMethylation450 BeadChip (450K) has been accepted as one of the most efficient technologies. However, challenges exist in analysis of DNA methylation data generated by this technology due to widespread biases. Results Here we proposed a generalized framework for evaluating data analysis methods for Illumina 450K array. This framework considers the following steps towards a successful analysis: importing data, quality control, within-array normalization, correcting type bias, detecting differentially methylated probes or regions and biological interpretation. Conclusions We evaluated five methods using three real datasets, and proposed outperform methods for the Illumina 450K array data analysis. Minfi and methylumi are optimal choice when analyzing small dataset. BMIQ and RCP are proper to correcting type bias and the normalized result of them can be used to discover DMPs. R package missMethyl is suitable for GO term enrichment analysis and biological interpretation.
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Affiliation(s)
- Zhenxing Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - XiaoLiang Wu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Yadong Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, 150001, China.
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746
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Geraghty AA, Sexton-Oates A, O’Brien EC, Alberdi G, Fransquet P, Saffery R, McAuliffe FM. A Low Glycaemic Index Diet in Pregnancy Induces DNA Methylation Variation in Blood of Newborns: Results from the ROLO Randomised Controlled Trial. Nutrients 2018; 10:nu10040455. [PMID: 29642382 PMCID: PMC5946240 DOI: 10.3390/nu10040455] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/28/2018] [Accepted: 04/04/2018] [Indexed: 11/30/2022] Open
Abstract
The epigenetic profile of the developing fetus is sensitive to environmental influence. Maternal diet has been shown to influence DNA methylation patterns in offspring, but research in humans is limited. We investigated the impact of a low glycaemic index dietary intervention during pregnancy on offspring DNA methylation patterns using a genome-wide methylation approach. Sixty neonates were selected from the ROLO (Randomised cOntrol trial of LOw glycaemic index diet to prevent macrosomia) study: 30 neonates from the low glycaemic index intervention arm and 30 from the control, whose mothers received no specific dietary advice. DNA methylation was investigated in 771,484 CpG sites in free DNA from cord blood serum. Principal component analysis and linear regression were carried out comparing the intervention and control groups. Gene clustering and pathway analysis were also explored. Widespread variation was identified in the newborns exposed to the dietary intervention, accounting for 11% of the total level of DNA methylation variation within the dataset. No association was found with maternal early-pregnancy body mass index (BMI), infant sex, or birthweight. Pathway analysis identified common influences of the intervention on gene clusters plausibly linked to pathways targeted by the intervention, including cardiac and immune functioning. Analysis in 60 additional samples from the ROLO study failed to replicate the original findings. Using a modest-sized discovery sample, we identified preliminary evidence of differential methylation in progeny of mothers exposed to a dietary intervention during pregnancy.
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Affiliation(s)
- Aisling A. Geraghty
- UCD Perinatal Research Centre, Obstetrics and Gynaecology, School of Medicine, University College Dublin, National Maternity Hospital, Dublin 2, Ireland; (A.A.G.); (E.C.O.); (G.A.)
| | - Alexandra Sexton-Oates
- Cancer and Disease Epigenetics, Murdoch Children’s Research Institute, Melbourne, Victoria 3052, Australia; (A.S.-O.); (P.F.); (R.S.)
| | - Eileen C. O’Brien
- UCD Perinatal Research Centre, Obstetrics and Gynaecology, School of Medicine, University College Dublin, National Maternity Hospital, Dublin 2, Ireland; (A.A.G.); (E.C.O.); (G.A.)
| | - Goiuri Alberdi
- UCD Perinatal Research Centre, Obstetrics and Gynaecology, School of Medicine, University College Dublin, National Maternity Hospital, Dublin 2, Ireland; (A.A.G.); (E.C.O.); (G.A.)
| | - Peter Fransquet
- Cancer and Disease Epigenetics, Murdoch Children’s Research Institute, Melbourne, Victoria 3052, Australia; (A.S.-O.); (P.F.); (R.S.)
| | - Richard Saffery
- Cancer and Disease Epigenetics, Murdoch Children’s Research Institute, Melbourne, Victoria 3052, Australia; (A.S.-O.); (P.F.); (R.S.)
- Department of Paediatrics, University of Melbourne, Victoria 3010, Australia
| | - Fionnuala M. McAuliffe
- UCD Perinatal Research Centre, Obstetrics and Gynaecology, School of Medicine, University College Dublin, National Maternity Hospital, Dublin 2, Ireland; (A.A.G.); (E.C.O.); (G.A.)
- Correspondence: ; Tel.: +353-1-63732
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747
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Heylen L, Thienpont B, Naesens M, Busschaert P, Depreeuw J, Smeets D, Jochmans I, Monbaliu D, Pirenne J, Lerut E, Ghesquiere B, Kuypers D, Lambrechts D, Sprangers B. Ischemia-Induced DNA Hypermethylation during Kidney Transplant Predicts Chronic Allograft Injury. J Am Soc Nephrol 2018; 29:1566-1576. [PMID: 29610404 DOI: 10.1681/asn.2017091027] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/26/2018] [Indexed: 12/28/2022] Open
Abstract
Background Ischemia during kidney transplant causes chronic allograft injury and adversely affects outcome, but the underlying mechanisms are incompletely understood. In tumors, oxygen shortage reduces the DNA demethylating activity of the ten-11 translocation (TET) enzymes, yielding hypermethylated genomes that promote tumor progression. We investigated whether ischemia similarly induces DNA hypermethylation in kidney transplants and contributes to chronic injury.Methods We profiled genome-wide DNA methylation in three cohorts of brain-dead donor kidney allograft biopsy specimens: a longitudinal cohort with paired biopsy specimens obtained at allograft procurement (preischemia; n=13), after implantation and reperfusion (postischemia; n=13), and at 3 or 12 months after transplant (n=5 each); a cross-sectional cohort with preimplantation biopsy specimens (n=82); and a cross-sectional cohort with postreperfusion biopsy specimens (n=46).Results Analysis of the paired preischemia and postischemia specimens revealed that methylation increased drastically in all allografts on ischemia. Hypermethylation was caused by loss of 5-hydroxymethylcytosine, the product of TET activity, and it was stable 1 year after transplant. In the preimplantation cohort, CpG hypermethylation directly correlated with ischemia time and for some CpGs, increased 2.6% per additional hour of ischemia. Hypermethylation preferentially affected and reduced the expression of genes involved in suppressing kidney injury and fibrosis. Moreover, CpG hypermethylation in preimplantation specimens predicted chronic injury, particularly fibrosis and glomerulosclerosis, 1 year after transplant. This finding was validated in the independent postreperfusion cohort, in which hypermethylation also predicted reduced allograft function 1 year after transplant, outperforming established clinical variables.Conclusions We highlight a novel epigenetic basis for ischemia-induced chronic allograft injury with biomarker potential.
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Affiliation(s)
- Line Heylen
- Departments of Nephrology.,Laboratories of Experimental Transplantation.,Laboratory for Translational Genetics, Department of Human Genetics, and
| | - Bernard Thienpont
- Laboratory for Translational Genetics, Department of Human Genetics, and.,VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | | | - Pieter Busschaert
- VIB Center for Cancer Biology, VIB, Leuven, Belgium.,Division of Gynaecological Oncology, Leuven Cancer Institute, University of Leuven, Belgium; and
| | - Jeroen Depreeuw
- VIB Center for Cancer Biology, VIB, Leuven, Belgium.,Division of Gynaecological Oncology, Leuven Cancer Institute, University of Leuven, Belgium; and
| | - Dominiek Smeets
- Laboratory for Translational Genetics, Department of Human Genetics, and.,VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Ina Jochmans
- Abdominal Transplantation, Department of Microbiology and Immunology.,Abdominal Transplant Surgery, and
| | - Diethard Monbaliu
- Abdominal Transplantation, Department of Microbiology and Immunology.,Abdominal Transplant Surgery, and
| | - Jacques Pirenne
- Abdominal Transplantation, Department of Microbiology and Immunology.,Abdominal Transplant Surgery, and
| | - Evelyne Lerut
- Pathology, University Hospitals Leuven, Leuven, Belgium
| | | | | | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, and .,VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Ben Sprangers
- Departments of Nephrology.,Laboratories of Experimental Transplantation
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748
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Barker ED, Walton E, Cecil CAM. Annual Research Review: DNA methylation as a mediator in the association between risk exposure and child and adolescent psychopathology. J Child Psychol Psychiatry 2018; 59:303-322. [PMID: 28736860 DOI: 10.1111/jcpp.12782] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/17/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND DNA methylation (DNAm) is a potential mechanism for propagating the effects of environmental exposures on child and adolescent mental health. In recent years, this field has experienced steady growth. METHODS We provide a strategic review of the current child and adolescent literature to evaluate evidence for a mediating role of DNAm in the link between environmental risks and psychopathological outcomes, with a focus on internalising and externalising difficulties. RESULTS Based on the studies presented, we conclude that there is preliminary evidence to support that (a) environmental factors, such as diet, neurotoxic exposures and stress, influence offspring DNAm, and that (b) variability in DNAm, in turn, is associated with child and adolescent psychopathology. Overall, very few studies have examined DNAm in relation to both exposures and outcomes, and almost all analyses have been correlational in nature. CONCLUSIONS DNAm holds potential as a biomarker indexing both environmental risk exposure and vulnerability for child psychopathology. However, the extent to which it may represent a causal mediator is not clear. In future, collection of prospective risk exposure, DNAm and outcomes - as well as functional characterisation of epigenetic findings - will assist in determining the role of DNAm in the link between risk exposure and psychopathology.
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Affiliation(s)
- Edward D Barker
- Department of Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Esther Walton
- Department of Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Charlotte A M Cecil
- Department of Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
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749
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Kular L, Kular S. Epigenetics applied to psychiatry: Clinical opportunities and future challenges. Psychiatry Clin Neurosci 2018; 72:195-211. [PMID: 29292553 DOI: 10.1111/pcn.12634] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/12/2017] [Accepted: 12/26/2017] [Indexed: 12/11/2022]
Abstract
Psychiatric disorders are clinically heterogeneous and debilitating chronic diseases resulting from a complex interplay between gene variants and environmental factors. Epigenetic processes, such as DNA methylation and histone posttranslational modifications, instruct the cell/tissue to correctly interpret external signals and adjust its functions accordingly. Given that epigenetic modifications are sensitive to environment, stable, and reversible, epigenetic studies in psychiatry could represent a promising approach to better understanding and treating disease. In the present review, we aim to discuss the clinical opportunities and challenges arising from the epigenetic research in psychiatry. Using selected examples, we first recapitulate key findings supporting the role of adverse life events, alone or in combination with genetic risk, in epigenetic programming of neuropsychiatric systems. Epigenetic studies further report encouraging findings about the use of methylation changes as diagnostic markers of disease phenotype and predictive tools of progression and response to treatment. Then we discuss the potential of using targeted epigenetic pharmacotherapy, combined with psychosocial interventions, for future personalized medicine for patients. Finally, we review the methodological limitations that could hinder interpretation of epigenetic data in psychiatry. They mainly arise from heterogeneity at the individual and tissue level and require future strategies in order to reinforce the biological relevance of epigenetic data and its translational use in psychiatry. Overall, we suggest that epigenetics could provide new insights into a more comprehensive interpretation of mental illness and might eventually improve the nosology, treatment, and prevention of psychiatric disorders.
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Affiliation(s)
- Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sonia Kular
- Adult Psychiatry Unit of Laval Secteur Est, Laval, France
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750
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Epigenetic Modifications as Biomarkers of Tumor Development, Therapy Response, and Recurrence across the Cancer Care Continuum. Cancers (Basel) 2018; 10:cancers10040101. [PMID: 29614786 PMCID: PMC5923356 DOI: 10.3390/cancers10040101] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/23/2018] [Accepted: 03/27/2018] [Indexed: 02/06/2023] Open
Abstract
Aberrant epigenetic modifications are an early event in carcinogenesis, with the epigenetic landscape continuing to change during tumor progression and metastasis—these observations suggest that specific epigenetic modifications could be used as diagnostic and prognostic biomarkers for many cancer types. DNA methylation, post-translational histone modifications, and non-coding RNAs are all dysregulated in cancer and are detectable to various degrees in liquid biopsies such as sputum, urine, stool, and blood. Here, we will focus on the application of liquid biopsies, as opposed to tissue biopsies, because of their potential as non-invasive diagnostic tools and possible use in monitoring therapy response and progression to metastatic disease. This includes a discussion of septin-9 (SEPT9) DNA hypermethylation for detecting colorectal cancer, which is by far the most developed epigenetic biomarker assay. Despite their potential as prognostic and diagnostic biomarkers, technical issues such as inconsistent methodology between studies, overall low yield of epigenetic material in samples, and the need for improved histone and non-coding RNA purification methods are limiting the use of epigenetic biomarkers. Once these technical limitations are overcome, epigenetic biomarkers could be used to monitor cancer development, disease progression, therapeutic response, and recurrence across the entire cancer care continuum.
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